3IGH | pdb_00003igh

Crystal structure of an uncharacterized metal-dependent hydrolase from pyrococcus horikoshii ot3

PDB DOI: https://doi.org/10.2210/pdb3IGH/pdb

Classification: HYDROLASE
Organism(s): Pyrococcus horikoshii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-07-27 Released: 2009-08-04
Deposition Author(s): Patskovsky, Y., Toro, R., Freeman, J., Miller, S., Sauder, J.M., Raushel, F.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.212 (Depositor), 0.210 (DCC)
R-Value Work:
0.178 (Depositor), 0.178 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of an Uncharacterized Metal-Dependent Hydrolase from Pyrococcus Horikoshii

Patskovsky, Y., Toro, R., Freeman, J., Miller, S., Sauder, J.M., Raushel, F.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 56.68 kDa
Atom Count: 4,459
Modeled Residue Count: 483
Deposited Residue Count: 486
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UNCHARACTERIZED METAL-DEPENDENT HYDROLASE	A [auth X]	486	Pyrococcus horikoshii	Mutation(s): 0 Gene Names: COG1574
UniProt
Find proteins for O58866 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58866 Go to UniProtKB: O58866
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O58866
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth X] SDF format, chain S [auth X] SDF format, chain R [auth X] SDF format, chain Q [auth X] SDF format, chain P [auth X] SDF format, chain O [auth X] SDF format, chain N [auth X] SDF format, chain M [auth X] SDF format, chain L [auth X] SDF format, chain K [auth X] SDF format, chain J [auth X] SDF format, chain I [auth X] SDF format, chain H [auth X] SDF format, chain G [auth X] SDF format, chain F [auth X] SDF format, chain E [auth X] SDF format, chain D [auth X] SDF format, chain C [auth X] SDF format, chain B [auth X] MOL2 format, chain T [auth X] MOL2 format, chain S [auth X] MOL2 format, chain R [auth X] MOL2 format, chain Q [auth X] MOL2 format, chain P [auth X] MOL2 format, chain O [auth X] MOL2 format, chain N [auth X] MOL2 format, chain M [auth X] MOL2 format, chain L [auth X] MOL2 format, chain K [auth X] MOL2 format, chain J [auth X] MOL2 format, chain I [auth X] MOL2 format, chain H [auth X] MOL2 format, chain G [auth X] MOL2 format, chain F [auth X] MOL2 format, chain E [auth X] MOL2 format, chain D [auth X] MOL2 format, chain C [auth X] MOL2 format, chain B [auth X] mmCIF format, chain T [auth X] mmCIF format, chain S [auth X] mmCIF format, chain R [auth X] mmCIF format, chain Q [auth X] mmCIF format, chain P [auth X] mmCIF format, chain O [auth X] mmCIF format, chain N [auth X] mmCIF format, chain M [auth X] mmCIF format, chain L [auth X] mmCIF format, chain K [auth X] mmCIF format, chain J [auth X] mmCIF format, chain I [auth X] mmCIF format, chain H [auth X] mmCIF format, chain G [auth X] mmCIF format, chain F [auth X] mmCIF format, chain E [auth X] mmCIF format, chain D [auth X] mmCIF format, chain C [auth X] mmCIF format, chain B [auth X]	B [auth X] C [auth X] D [auth X] E [auth X] F [auth X] B [auth X], C [auth X], D [auth X], E [auth X], F [auth X], G [auth X], H [auth X], I [auth X], J [auth X], K [auth X], L [auth X], M [auth X], N [auth X], O [auth X], P [auth X], Q [auth X], R [auth X], S [auth X], T [auth X]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth X] Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Focus chain J [auth X] Focus chain K [auth X] Focus chain L [auth X] Focus chain M [auth X] Focus chain N [auth X] Focus chain O [auth X] Focus chain P [auth X] Focus chain Q [auth X] Focus chain R [auth X] Focus chain S [auth X] Focus chain T [auth X] Interactions & Density Focus chain B [auth X] Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Focus chain J [auth X] Focus chain K [auth X] Focus chain L [auth X] Focus chain M [auth X] Focus chain N [auth X] Focus chain O [auth X] Focus chain P [auth X] Focus chain Q [auth X] Focus chain R [auth X] Focus chain S [auth X] Focus chain T [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.212 (Depositor), 0.210 (DCC)
R-Value Work: 0.178 (Depositor), 0.178 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.571	α = 90
b = 106.571	β = 90
c = 133.174	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-08-04

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-08-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-11-21
Changes: Data collection, Structure summary
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-02-21
Changes: Data collection, Database references