3ORP | pdb_00003orp

Mycobacterium tuberculosis PknB kinase domain L33D mutant (crystal form 5)

PDB DOI: https://doi.org/10.2210/pdb3ORP/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis H37Ra
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-09-07 Released: 2010-12-15
Deposition Author(s): Good, M.C., Echols, N., Lombana, T.N., Alber, T., TB Structural Genomics Consortium (TBSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.238 (Depositor), 0.244 (DCC)
R-Value Work:
0.188 (Depositor), 0.197 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3ORP

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Allosteric activation mechanism of the Mycobacterium tuberculosis receptor Ser/Thr kinase, PknB

Lombana, T.N., Echols, N., Good, M.C., Thomsen, N.D., Ng, H.-L., Greenstein, A.E., Falick, A.M., King, D.S., Alber, T.

(2010) Structure 18: 1667-1677

Macromolecule Content

Total Structure Weight: 34.04 kDa
Atom Count: 2,242
Modeled Residue Count: 274
Deposited Residue Count: 311
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine protein kinase	A	311	Mycobacterium tuberculosis H37Ra	Mutation(s): 1 Gene Names: MRA_0016, pknB, PknB (Rv0014c) EC: 2.7.11.1
UniProt
Find proteins for P9WI81 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WI81 Go to UniProtKB: P9WI81
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WI81
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS Query on AGS 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]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.238 (Depositor), 0.244 (DCC)
R-Value Work: 0.188 (Depositor), 0.197 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.185	α = 90
b = 52.164	β = 90
c = 155.652	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
EPMR	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-12-15

Deposition Author(s):

TB Structural Genomics Consortium (TBSGC)

Revision History (Full details and data files)

Version 1.0: 2010-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-06
Changes: Database references, Derived calculations
Version 1.3: 2023-09-06
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.