3D7R | pdb_00003d7r

Crystal structure of a putative esterase from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb3D7R/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus subsp. aureus USA300_TCH1516
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-05-21 Released: 2009-06-09
Deposition Author(s): Lam, R., Battaile, K.P., Chan, T., Romanov, V., Lam, K., Soloveychik, M., Wu-Brown, J., Pai, E.F., Chirgadze, N.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.192 (Depositor), 0.195 (DCC)
R-Value Work:
0.158 (Depositor), 0.161 (DCC)
R-Value Observed:
0.160 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a putative esterase from Staphylococcus aureus

Battaile, K.P., Lam, R., Chan, T., Romanov, V., Lam, K., Soloveychik, M., Wu-Brown, J., Pai, E.F., Chirgadze, N.Y.

To be published.

Macromolecule Content

Total Structure Weight: 78.95 kDa
Atom Count: 5,227
Modeled Residue Count: 591
Deposited Residue Count: 652
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase	A, B	326	Staphylococcus aureus subsp. aureus USA300_TCH1516	Mutation(s): 0 Gene Names: USA300HOU_2331 EC: 3.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain FA [auth B] SDF format, chain EA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B]	EA [auth B], FA [auth B], P [auth A], Q [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain P [auth A] Focus chain Q [auth A]
BR Query on BR Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain C [auth A] MOL2 format, chain R [auth B] MOL2 format, chain C [auth A] mmCIF format, chain R [auth B] mmCIF format, chain C [auth A]	C [auth A], R [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain R [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] F [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain D [auth A] MOL2 format, chain S [auth B] MOL2 format, chain D [auth A] mmCIF format, chain S [auth B] mmCIF format, chain D [auth A]	D [auth A], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain S [auth B] Interactions & Density Focus chain D [auth A] Focus chain S [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain E [auth A] MOL2 format, chain T [auth B] MOL2 format, chain E [auth A] mmCIF format, chain T [auth B] mmCIF format, chain E [auth A]	E [auth A], T [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain T [auth B] Interactions & Density Focus chain E [auth A] Focus chain T [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	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: 0.192 (Depositor), 0.195 (DCC)
R-Value Work: 0.158 (Depositor), 0.161 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.888	α = 80.82
b = 46.412	β = 89.97
c = 91.688	γ = 69.51

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-06-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-06-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary