3L21 | pdb_00003l21

The crystal structure of a dimeric mutant of dihydrodipicolinate synthase (DAPA, RV2753C) from Mycobacterium Tuberculosis - DHDPS-A204R

PDB DOI: https://doi.org/10.2210/pdb3L21/pdb

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

Deposited: 2009-12-14 Released: 2010-12-15
Deposition Author(s): Evans, G.L., Schuldt, L., Jamerson, G.B., Devenish, S.R., Weiss, M.S., Gerrard, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.204 (Depositor), 0.206 (DCC)
R-Value Work:
0.178 (Depositor)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

A dimeric mutant of DHDPS from Mycobacterium tuberculosis

Evans, G.L., Schuldt, L., Griffin, M.D., Perugini, M.A., Jamerson, G.B., Devenish, S.R., Weiss, M.S., Gerrard, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 193.36 kDa
Atom Count: 14,886
Modeled Residue Count: 1,772
Deposited Residue Count: 1,824
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B, C, D, E A, B, C, D, E, F	304	Mycobacterium tuberculosis	Mutation(s): 1 Gene Names: dapA, MT2823, MTV002.18c, Rv2753c EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for P9WP25 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WP25 Go to UniProtKB: P9WP25
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WP25
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain FB [auth F] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain GB [auth F] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain WA [auth E] SDF format, chain XA [auth E] SDF format, chain YA [auth E] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth F] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth F] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain XA [auth E] MOL2 format, chain YA [auth E] mmCIF format, chain FA [auth C] mmCIF format, chain FB [auth F] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth F] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain XA [auth E] mmCIF format, chain YA [auth E]	FA [auth C] FB [auth F] G [auth A] GA [auth C] GB [auth F] FA [auth C], FB [auth F], G [auth A], GA [auth C], GB [auth F], H [auth A], HA [auth C], I [auth A], OA [auth D], PA [auth D], R [auth B], S [auth B], T [auth B], WA [auth E], XA [auth E], YA [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain FA [auth C] Focus chain FB [auth F] Focus chain G [auth A] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth E] Interactions & Density Focus chain FA [auth C] Focus chain FB [auth F] Focus chain G [auth A] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain CB [auth E] SDF format, chain DB [auth E] SDF format, chain EA [auth B] SDF format, chain IA [auth C] SDF format, chain IB [auth F] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain JB [auth F] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain KB [auth F] SDF format, chain LA [auth C] SDF format, chain LB [auth F] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain TA [auth D] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Z [auth B] SDF format, chain ZA [auth E] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth E] MOL2 format, chain DB [auth E] MOL2 format, chain EA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth F] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain JB [auth F] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain KB [auth F] MOL2 format, chain LA [auth C] MOL2 format, chain LB [auth F] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth E] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth E] mmCIF format, chain DB [auth E] mmCIF format, chain EA [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain IB [auth F] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain JB [auth F] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain KB [auth F] mmCIF format, chain LA [auth C] mmCIF format, chain LB [auth F] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth E]	CA [auth B] CB [auth E] DB [auth E] EA [auth B] IA [auth C] CA [auth B], CB [auth E], DB [auth E], EA [auth B], IA [auth C], IB [auth F], J [auth A], JA [auth C], JB [auth F], K [auth A], KA [auth C], KB [auth F], LA [auth C], LB [auth F], NA [auth C], O [auth A], P [auth A], QA [auth D], RA [auth D], SA [auth D], TA [auth D], U [auth B], V [auth B], W [auth B], Z [auth B], ZA [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EA [auth B] Focus chain IA [auth C] Focus chain IB [auth F] Focus chain J [auth A] Focus chain JA [auth C] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KA [auth C] Focus chain KB [auth F] Focus chain LA [auth C] Focus chain LB [auth F] Focus chain NA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain Z [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain CA [auth B] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EA [auth B] Focus chain IA [auth C] Focus chain IB [auth F] Focus chain J [auth A] Focus chain JA [auth C] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KA [auth C] Focus chain KB [auth F] Focus chain LA [auth C] Focus chain LB [auth F] Focus chain NA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain Z [auth B] Focus chain ZA [auth E]
PYR Query on PYR Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] MOL2 format, chain DA [auth B] mmCIF format, chain DA [auth B]	DA [auth B]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Interactions & Density Focus chain DA [auth B]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth E] SDF format, chain BA [auth B] SDF format, chain BB [auth E] SDF format, chain HB [auth F] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth E] MOL2 format, chain HB [auth F] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth E] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth E] mmCIF format, chain HB [auth F] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	AA [auth B] AB [auth E] BA [auth B] BB [auth E] HB [auth F] AA [auth B], AB [auth E], BA [auth B], BB [auth E], HB [auth F], L [auth A], M [auth A], MA [auth C], N [auth A], X [auth B], Y [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain AB [auth E] Focus chain BA [auth B] Focus chain BB [auth E] Focus chain HB [auth F] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth E] Focus chain BA [auth B] Focus chain BB [auth E] Focus chain HB [auth F] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain X [auth B] Focus chain Y [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain EB [auth E] SDF format, chain UA [auth D] SDF format, chain VA [auth D] MOL2 format, chain EB [auth E] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] mmCIF format, chain EB [auth E] mmCIF format, chain UA [auth D] mmCIF format, chain VA [auth D]	EB [auth E], UA [auth D], VA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EB [auth E] Focus chain UA [auth D] Focus chain VA [auth D] Interactions & Density Focus chain EB [auth E] Focus chain UA [auth D] Focus chain VA [auth D]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS
KPI Query on KPI	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₉ H₁₆ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.204 (Depositor), 0.206 (DCC)
R-Value Work: 0.178 (Depositor)
R-Value Observed: 0.179 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.83	α = 90
b = 188.83	β = 90
c = 130.43	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-12-15

Deposition Author(s):

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: 2018-05-16
Changes: Data collection, Refinement description
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection
Version 2.1: 2023-11-29
Changes: Data collection