1U13 | pdb_00001u13

Crystal structure analysis of the C37L/C151T/C442A-triple mutant of CYP51 from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb1U13/pdb

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

Deposited: 2004-07-14 Released: 2004-07-27
Deposition Author(s): Podust, L.M., Yermalitskaya, L.V., Kim, Y., Waterman, M.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.241 (Depositor), 0.230 (DCC)
R-Value Work:
0.200 (Depositor), 0.190 (DCC)
R-Value Observed:
0.200 (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

Crystal structure analysis of the C37L/C151T/C442A-triple mutant of CYP51 from Mycobacterium tuberculosis

Podust, L.M., Yermalitskaya, L.V., Kim, Y., Waterman, M.R.

To be published.

Macromolecule Content

Total Structure Weight: 52.09 kDa
Atom Count: 3,685
Modelled Residue Count: 433
Deposited Residue Count: 455
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 51	A	455	Mycobacterium tuberculosis	Mutation(s): 3 Gene Names: Name=cyp51, OrderedLocusNames=Rv0764c, MT0788 EC: 1.14.13.70 (PDB Primary Data), 1.14.15.36 (UniProt)
UniProt
Find proteins for P9WPP9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPP9 Go to UniProtKB: P9WPP9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPP9
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM 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]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.241 (Depositor), 0.230 (DCC)
R-Value Work: 0.200 (Depositor), 0.190 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.294	α = 90
b = 85.133	β = 90
c = 110.464	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-07-27

Deposition Author(s):

Yermalitskaya, L.V.

Revision History (Full details and data files)

Version 1.0: 2004-07-27
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-10-27
Changes: Database references, Derived calculations
Version 1.4: 2023-08-23
Changes: Data collection, Refinement description

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.