6BLB | pdb_00006blb

1.88 Angstrom Resolution Crystal Structure Holliday Junction ATP-dependent DNA Helicase (RuvB) from Pseudomonas aeruginosa in Complex with ADP

PDB DOI: https://doi.org/10.2210/pdb6BLB/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-11-09 Released: 2017-11-22
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Kiryukhina, O., Grimshaw, S., Kwon, K., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.213 (Depositor), 0.220 (DCC)
R-Value Work:
0.172 (Depositor), 0.180 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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 : 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: 39.83 kDa
Atom Count: 2,751
Modeled Residue Count: 311
Deposited Residue Count: 355
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Holliday junction ATP-dependent DNA helicase RuvB	A	355	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: ruvB, PA0967 EC: 3.6.4.12 (PDB Primary Data), 3.6.4 (UniProt)
UniProt
Find proteins for Q51426 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q51426 Go to UniProtKB: Q51426
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q51426
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.213 (Depositor), 0.220 (DCC)
R-Value Work: 0.172 (Depositor), 0.180 (DCC)
R-Value Observed: 0.175 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36blb

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.537	α = 90
b = 85.537	β = 90
c = 77.103	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MoRDa	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-11-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2017-11-22
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.2: 2025-06-18
Changes: Database references, Structure summary