2AE8 | pdb_00002ae8

Crystal Structure of Imidazoleglycerol-phosphate Dehydratase from Staphylococcus aureus subsp. aureus N315

PDB DOI: https://doi.org/10.2210/pdb2AE8/pdb

Classification: LYASE
Organism(s): Staphylococcus aureus subsp. aureus N315
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-07-21 Released: 2005-09-06
Deposition Author(s): Kim, Y., Quartey, P., Holzle, D., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.226 (Depositor), 0.225 (DCC)
R-Value Work:
0.188 (Depositor), 0.187 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of Imidazoleglycerol-phosphate Dehydratase from Staphylococcus aureus subsp. aureus N315

Kim, Y., Quartey, P., Holzle, D., Collart, F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 149.46 kDa
Atom Count: 9,237
Modeled Residue Count: 1,026
Deposited Residue Count: 1,326
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Imidazoleglycerol-phosphate dehydratase	A, B, C, D, E A, B, C, D, E, F	221	Staphylococcus aureus subsp. aureus N315	Mutation(s): 0 EC: 4.2.1.19
UniProt
Find proteins for P64373 (Staphylococcus aureus (strain N315)) Explore P64373 Go to UniProtKB: P64373
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P64373
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain P [auth D] SDF format, chain V [auth F] SDF format, chain U [auth F] SDF format, chain T [auth F] SDF format, chain S [auth E] SDF format, chain R [auth E] SDF format, chain Q [auth E] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth D] MOL2 format, chain V [auth F] MOL2 format, chain U [auth F] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth D] mmCIF format, chain V [auth F] mmCIF format, chain U [auth F] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth B] K [auth B] G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth C], N [auth C], O [auth C], P [auth D], Q [auth E], R [auth E], S [auth E], T [auth F], U [auth F], V [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.226 (Depositor), 0.225 (DCC)
R-Value Work: 0.188 (Depositor), 0.187 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.247	α = 90
b = 129.247	β = 90
c = 180.143	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
SCALEPACK	data scaling
SHELX	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-09-06

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2005-09-06
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2015-05-20
Changes: Database references, Derived calculations, Other
Version 1.4: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary