3ICJ | pdb_00003icj

Crystal structure of an uncharacterized metal-dependent hydrolase from pyrococcus furiosus

PDB DOI: https://doi.org/10.2210/pdb3ICJ/pdb
Entry: 3ICJ supersedes: 3ETK

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

Deposited: 2009-07-17 Released: 2009-07-28
Deposition Author(s): Bonanno, J.B., Patskovsky, Y., Freeman, J., Bain, K.T., Hu, S., Ozyurt, S., Wasserman, 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:
0.267 (Depositor), 0.280 (DCC)
R-Value Work:
0.207 (Depositor), 0.221 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

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

Bonanno, J.B., Patskovsky, Y., Freeman, J., Bain, K.T., Hu, S., Ozyurt, S., Wasserman, S., Sauder, J.M., Raushel, F.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 60.51 kDa
Atom Count: 4,070
Modeled Residue Count: 468
Deposited Residue Count: 534
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	534	Pyrococcus furiosus	Mutation(s): 0 Gene Names: PF0846
UniProt
Find proteins for Q8U2I8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U2I8 Go to UniProtKB: Q8U2I8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U2I8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.267 (Depositor), 0.280 (DCC)
R-Value Work: 0.207 (Depositor), 0.221 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.869	α = 90
b = 116.438	β = 90
c = 169.66	γ = 90

Software Package:

Software Name	Purpose
SHELXCD	phasing
SHELXE	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-07-28

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

This entry supersedes: 3ETK

Revision History (Full details and data files)

Version 1.0: 2009-07-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2018-11-21
Changes: Data collection, Structure summary
Version 1.4: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2025-03-26
Changes: Data collection, Database references, Structure summary