3FSG | pdb_00003fsg

Crystal structure of alpha/beta superfamily hydrolase from Oenococcus oeni PSU-1

PDB DOI: https://doi.org/10.2210/pdb3FSG/pdb

Classification: HYDROLASE
Organism(s): Oenococcus oeni PSU-1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-09 Released: 2009-01-27
Deposition Author(s): Nocek, B., Bigelow, L., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.225 (Depositor), 0.204 (DCC)
R-Value Work:
0.180 (Depositor), 0.198 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of alpha/beta superfamily hydrolase from Oenococcus oeni PSU-1

Nocek, B., Bigelow, L., Cobb, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 126.89 kDa
Atom Count: 9,199
Modeled Residue Count: 1,063
Deposited Residue Count: 1,088
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta superfamily hydrolase	A, B, C	272	Oenococcus oeni PSU-1	Mutation(s): 0 Gene Names: OEOE_1827
UniProt
Find proteins for Q04D10 (Oenococcus oeni (strain ATCC BAA-331 / PSU-1)) Explore Q04D10 Go to UniProtKB: Q04D10
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q04D10
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta superfamily hydrolase	D	272	Oenococcus oeni PSU-1	Mutation(s): 0 Gene Names: OEOE_1827
UniProt
Find proteins for Q04D10 (Oenococcus oeni (strain ATCC BAA-331 / PSU-1)) Explore Q04D10 Go to UniProtKB: Q04D10
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q04D10
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain V [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain V [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] L [auth B] N [auth C] O [auth C] H [auth A], I [auth A], L [auth B], N [auth C], O [auth C], P [auth C], V [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain V [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain G [auth A] MOL2 format, chain R [auth D] MOL2 format, chain G [auth A] mmCIF format, chain R [auth D] mmCIF format, chain G [auth A]	G [auth A], R [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain R [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] K [auth B] M [auth C] S [auth D] E [auth A], F [auth A], K [auth B], M [auth C], S [auth D], T [auth D], U [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain J [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain J [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain J [auth A]	J [auth A], Q [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain Q [auth C] Interactions & Density Focus chain J [auth A] Focus chain Q [auth C]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A, B, C	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.225 (Depositor), 0.204 (DCC)
R-Value Work: 0.180 (Depositor), 0.198 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 217.493	α = 90
b = 40.58	β = 107.5
c = 135.98	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
Coot	model building
MLPHARE	phasing
CCP4	model building
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
CCP4	phasing
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-01-27

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-01-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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Crystal structure of alpha/beta superfamily hydrolase from Oenococcus oeni PSU-1

Crystal structure of alpha/beta superfamily hydrolase from Oenococcus oeni PSU-1

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

3FSG | pdb_00003fsg