4U5Q | pdb_00004u5q

High resolution crystal structure of reductase (R) domain of nonribosomal peptide synthetase from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb4U5Q/pdb

Classification: LIGASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-07-25 Released: 2016-01-13
Deposition Author(s): Patel, K.D., Haque, A.S., Priyadarshan, K., Sankaranarayanan, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.245 (Depositor), 0.246 (DCC)
R-Value Work:
0.202 (Depositor), 0.207 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

High resolution structure of R-domain of nonribosomal peptide synthetase from Mycobacterium tuberculosis

Patel, K.D., Haque, A.S., Sankaranarayanan, R.

To be published.

Macromolecule Content

Total Structure Weight: 104.97 kDa
Atom Count: 7,239
Modeled Residue Count: 855
Deposited Residue Count: 956
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide synthetase	A, B	478	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: nrp, Rv0101, LH57_00575 EC: 2.3.1 (UniProt), 6.2.1 (UniProt)
UniProt
Find proteins for Q10896 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore Q10896 Go to UniProtKB: Q10896
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q10896
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XPE Query on XPE Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL C₂₀ H₄₂ O₁₁ DTPCFIHYWYONMD-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.245 (Depositor), 0.246 (DCC)
R-Value Work: 0.202 (Depositor), 0.207 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.532	α = 90
b = 88.593	β = 90
c = 126.077	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-01-13

Deposition Author(s):

Priyadarshan, K.

Sankaranarayanan, R.

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.