6CVE

Crystal structure of Mycobacterium tuberculosis dethiobiotin Synthetase in complex with cytidine triphosphate and 7,8-diaminopelargonic acid

PDB DOI: https://doi.org/10.2210/pdb6CVE/pdb

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

Deposited: 2018-03-28 Released: 2018-11-21
Deposition Author(s): Thompson, A.P., Bruning, J.B., Wegener, K.L., Polyak, S.W.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.271
R-Value Work: 0.194
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Mycobacterium tuberculosis Dethiobiotin Synthetase Facilitates Nucleoside Triphosphate Promiscuity through Alternate Binding Modes

Thompson, A.P., Salaemae, W., Pederick, J.L., Abell, A.D., Booker, G.W., Bruning, J.B., Polyak, S.W.

(2018) ACS Catal 8(11): 10774-10783

DOI: https://doi.org/10.1021/acscatal.8b03475

Macromolecule Content

Total Structure Weight: 96.3 kDa
Atom Count: 7,263
Modelled Residue Count: 908
Deposited Residue Count: 940
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent dethiobiotin synthetase BioD	A, B, C, D	235	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: bioD, Rv1570, MTCY336.33c EC: 6.3.3.3
UniProt
Find proteins for P9WPQ5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPQ5 Go to UniProtKB: P9WPQ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPQ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CTP (Subject of Investigation/LOI) Query on CTP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth C] mmCIF format, chain M [auth D]	E [auth A], I [auth C], M [auth D]	CYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₄ P₃ PCDQPRRSZKQHHS-XVFCMESISA-N		Interactions Focus chain E [auth A] Focus chain I [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth C] Focus chain M [auth D]
DSD (Subject of Investigation/LOI) Query on DSD Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] MOL2 format, chain G [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] mmCIF format, chain G [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C]	G [auth B], K [auth C], L [auth C]	7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID C₁₀ H₂₀ N₂ O₄ OQNJZSIPDMTUAJ-JGVFFNPUSA-N		Interactions Focus chain G [auth B] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain G [auth B] Focus chain K [auth C] Focus chain L [auth C]
FLC (Subject of Investigation/LOI) Query on FLC Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain N [auth D]	F [auth A], J [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.271
R-Value Work: 0.194
R-Value Observed: 0.198
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.81	α = 90
b = 103.841	β = 90
c = 152.62	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-11-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1068885

Revision History (Full details and data files)

Version 1.0: 2018-11-21
Type: Initial release
Version 1.1: 2020-01-08
Changes: Author supporting evidence
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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Help and Resources

6CVE

Crystal structure of Mycobacterium tuberculosis dethiobiotin Synthetase in complex with cytidine triphosphate and 7,8-diaminopelargonic acid

Mycobacterium tuberculosis Dethiobiotin Synthetase Facilitates Nucleoside Triphosphate Promiscuity through Alternate Binding Modes

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)