3NPG | pdb_00003npg

Crystal structure of a protein with unknown function from DUF364 family (PH1506) from PYROCOCCUS HORIKOSHII at 2.70 A resolution

PDB DOI: https://doi.org/10.2210/pdb3NPG/pdb

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

Deposited: 2010-06-28 Released: 2010-09-29
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.235 (Depositor), 0.261 (DCC)
R-Value Work:
0.204 (Depositor), 0.230 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of a protein with unknown function from DUF364 family (PH1506) from PYROCOCCUS HORIKOSHII at 2.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 114.16 kDa
Atom Count: 7,609
Modeled Residue Count: 980
Deposited Residue Count: 996
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized DUF364 family protein	A, B, C, D	249	Pyrococcus horikoshii	Mutation(s): 0 Gene Names: PH1506
UniProt
Find proteins for O59175 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59175 Go to UniProtKB: O59175
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O59175
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth C] SDF format, chain H [auth D] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D] mmCIF format, chain F [auth B]	E [auth A], F [auth B], G [auth C], H [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.235 (Depositor), 0.261 (DCC)
R-Value Work: 0.204 (Depositor), 0.230 (DCC)
R-Value Observed: 0.206 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.541	α = 90
b = 95.179	β = 90
c = 159.098	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
BUSTER-TNT	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Rosetta	phasing
PHASER	phasing
BUSTER	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-09-29

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-09-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2023-09-20
Changes: Data collection, Refinement description
Version 1.5: 2023-11-22
Changes: Data collection
Version 1.6: 2024-11-20
Changes: 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.