2GFQ

Structure of Protein of Unknown Function PH0006 from Pyrococcus horikoshii

PDB DOI: https://doi.org/10.2210/pdb2GFQ/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-03-22 Released: 2006-04-25
Deposition Author(s): Cuff, M.E., Skarina, T., Gorodichtchenskaia, E., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.179
R-Value Work: 0.150
R-Value Observed: 0.152

wwPDB Validation 3D Report Full Report

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

Literature

Structure of hypothetical protein ph0006 from Pyrococcus horikoshii

Cuff, M.E., Skarina, T., Gorodichtchenskaia, E., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 103.95 kDa
Atom Count: 7,927
Modelled Residue Count: 846
Deposited Residue Count: 894
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0204 protein PH0006	A, B, C	298	Pyrococcus horikoshii OT3	Mutation(s): 9 Gene Names: PH0006
UniProt
Find proteins for O57774 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57774 Go to UniProtKB: O57774
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O57774
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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: 1.75 Å
R-Value Free: 0.179
R-Value Work: 0.150
R-Value Observed: 0.152
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.021	α = 90
b = 67.029	β = 90.09
c = 111.572	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELX	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
Coot	model building
O	model building
ARP/wARP	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-04-25

Deposition Author(s):

Cuff, M.E.

Skarina, T.

Gorodichtchenskaia, E.

Edwards, A.

Savchenko, A.

Joachimiak, A.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2006-04-25
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance