5UME | pdb_00005ume

Crystal Structure of 5,10-Methylenetetrahydrofolate Reductase MetF from Haemophilus influenzae

PDB DOI: https://doi.org/10.2210/pdb5UME/pdb

Classification: OXIDOREDUCTASE
Organism(s): Haemophilus influenzae Rd KW20
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-01-27 Released: 2017-02-22
Deposition Author(s): Kim, Y., Mulligan, R., Maltseva, N., Grimshaw, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.169 (Depositor), 0.170 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.

Inniss, N.L., Minasov, G., Chang, C., Tan, K., Kim, Y., Maltseva, N., Stogios, P., Filippova, E., Michalska, K., Osipiuk, J., Jaroszewki, L., Godzik, A., Savchenko, A., Joachimiak, A., Anderson, W.F., Satchell, K.J.F.

(2025) Microbiol Resour Announc 14: e0020025-e0020025

PubMed: 40391899 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/mra.00200-25
Primary Citation of Related Structures:
5UME, 5USW, 5USX, 5UTX, 5UU6, 5UWY, 5UX9, 5WP0, 6AON, 6AOO, 6AZI, 6B5F, 6B8D, 6BK7, 6BLB, 6C8Q, 6PU9, 6PUA, 6PXA, 6W2Z

PubMed Abstract:
Antibiotic resistance remains a leading cause of severe infections worldwide. Small changes in protein sequence can impact antibiotic efficacy. Here, we report deposition of 58 X-ray crystal structures of bacterial proteins that are known targets for antibiotics, which expands knowledge of structural variation to support future antibiotic discovery or modifications.

Organizational Affiliation

Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.

Macromolecule Content

Total Structure Weight: 205.78 kDa
Atom Count: 13,964
Modeled Residue Count: 1,696
Deposited Residue Count: 1,770
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5,10-methylenetetrahydrofolate reductase	A, B, C, D, E A, B, C, D, E, F	295	Haemophilus influenzae Rd KW20	Mutation(s): 0 Gene Names: metF, HI_1444 EC: 1.5.1.20 (PDB Primary Data), 1.5.1.54 (UniProt)
UniProt
Find proteins for P45208 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P45208 Go to UniProtKB: P45208
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P45208
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain Z [auth F] SDF format, chain G [auth A] SDF format, chain X [auth E] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain Z [auth F] MOL2 format, chain G [auth A] MOL2 format, chain X [auth E] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain Z [auth F] mmCIF format, chain G [auth A] mmCIF format, chain X [auth E]	G [auth A] K [auth B] O [auth C] S [auth D] X [auth E] G [auth A], K [auth B], O [auth C], S [auth D], X [auth E], Z [auth F]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain X [auth E] Focus chain Z [auth F] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain X [auth E] Focus chain Z [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	H [auth A], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain J [auth A] MOL2 format, chain CA [auth F] MOL2 format, chain J [auth A] mmCIF format, chain CA [auth F] mmCIF format, chain J [auth A]	CA [auth F], J [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain J [auth A] Interactions & Density Focus chain CA [auth F] Focus chain J [auth A]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain I [auth A] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain Y [auth E] SDF format, chain M [auth B] SDF format, chain V [auth D] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain M [auth B] MOL2 format, chain V [auth D] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain R [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain M [auth B] mmCIF format, chain V [auth D]	AA [auth F] BA [auth F] I [auth A] M [auth B] R [auth C] AA [auth F], BA [auth F], I [auth A], M [auth B], R [auth C], T [auth D], U [auth D], V [auth D], Y [auth E]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain Y [auth E]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain W [auth D] SDF format, chain P [auth C] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth D] MOL2 format, chain P [auth C] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth D] mmCIF format, chain P [auth C]	N [auth B], P [auth C], Q [auth C], W [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain W [auth D] Interactions & Density Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.228 (Depositor), 0.230 (DCC)
R-Value Work: 0.169 (Depositor), 0.170 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.065	α = 90
b = 134.96	β = 90
c = 182.985	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-02-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2017-02-22
Type: Initial release
Version 1.1: 2017-09-13
Changes: Author supporting evidence
Version 1.2: 2022-04-13
Changes: Author supporting evidence, Database references
Version 1.3: 2023-10-04
Changes: Data collection, Refinement description
Version 1.4: 2025-06-25
Changes: Database references, Structure summary