3K6R | pdb_00003k6r

CRYSTAL STRUCTURE OF putative transferase PH0793 FROM PYROCOCCUS HORIKOSHII

PDB DOI: https://doi.org/10.2210/pdb3K6R/pdb
Entry: 3K6R supersedes: 2FRN

Classification: TRANSFERASE
Organism(s): Pyrococcus horikoshii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-10-09 Released: 2009-10-20
Deposition Author(s): Chang, C., Skarina, T., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.256 (Depositor), 0.284 (DCC)
R-Value Work:
0.211 (Depositor)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3K6R

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

Literature

Crystal Structure of Protein Ph0793 from Pyrococcus Horikoshii

Chang, C., Skarina, T., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 32.58 kDa
Atom Count: 2,209
Modeled Residue Count: 262
Deposited Residue Count: 278
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative transferase PH0793	A	278	Pyrococcus horikoshii	Mutation(s): 0 Gene Names: PH0793 EC: 2.5.1.114
UniProt
Find proteins for O58523 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58523 Go to UniProtKB: O58523
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O58523
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.256 (Depositor), 0.284 (DCC)
R-Value Work: 0.211 (Depositor)
R-Value Observed: 0.213 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.308	α = 90
b = 54.231	β = 100.02
c = 58.613	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	model building
ARP/wARP	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
RESOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-10-20

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

This entry supersedes: 2FRN

Revision History (Full details and data files)

Version 1.0: 2009-10-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.