6BLK | pdb_00006blk

Mycobacterial sensor histidine kinase MprB

PDB DOI: https://doi.org/10.2210/pdb6BLK/pdb

Classification: TRANSFERASE
Organism(s): Mycolicibacterium hassiacum DSM 44199
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2017-11-10 Released: 2017-11-22
Deposition Author(s): Li, J., Korotkova, N., Korotkov, K.V.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.221 (Depositor), 0.220 (DCC)
R-Value Work:
0.184 (Depositor), 0.180 (DCC)
R-Value Observed:
0.186 (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

Mycobacterial sensor histidine kinase MprB

Li, J., Korotkova, N., Korotkov, K.V.

To be published.

Macromolecule Content

Total Structure Weight: 70.66 kDa
Atom Count: 5,428
Modeled Residue Count: 613
Deposited Residue Count: 632
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal transduction histidine-protein kinase/phosphatase mprB	A [auth C], B [auth D], C [auth A], D [auth B]	158	Mycolicibacterium hassiacum DSM 44199	Mutation(s): 0 Gene Names: mprB, C731_3480 EC: 3.1.3 (PDB Primary Data), 2.7.13.3 (UniProt)
UniProt
Find proteins for K5BDW2 (Mycolicibacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849)) Explore K5BDW2 Go to UniProtKB: K5BDW2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K5BDW2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain K [auth B] SDF format, chain I [auth A] SDF format, chain G [auth D] MOL2 format, chain E [auth C] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain G [auth D] mmCIF format, chain E [auth C] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain G [auth D]	E [auth C], G [auth D], I [auth A], K [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth C] Focus chain G [auth D] Focus chain I [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth C] Focus chain G [auth D] Focus chain I [auth A] Focus chain K [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain H [auth D] SDF format, chain F [auth C] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain H [auth D] MOL2 format, chain F [auth C] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain H [auth D] mmCIF format, chain F [auth C]	F [auth C], H [auth D], J [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth C] Focus chain H [auth D] Focus chain J [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth C] Focus chain H [auth D] Focus chain J [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.221 (Depositor), 0.220 (DCC)
R-Value Work: 0.184 (Depositor), 0.180 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.41	α = 102.78
b = 61.63	β = 104.47
c = 67.22	γ = 109.08

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
BALBES	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-11-22

Deposition Author(s):

Li, J.

Korotkova, N.

Korotkov, K.V.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI119022
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM110787

Revision History (Full details and data files)

Version 1.0: 2017-11-22
Type: Initial release
Version 1.1: 2019-12-11
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description