1XX7

Conserved hypothetical protein from Pyrococcus furiosus Pfu-403030-001

PDB DOI: https://doi.org/10.2210/pdb1XX7/pdb

Classification: structural genomics, unknown function
Organism(s): Pyrococcus furiosus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-11-04 Released: 2004-12-28
Deposition Author(s): Chen, L., Tempel, W., Habel, J., Zhou, W., Nguyen, D., Chang, S.-H., Lee, D., Kelley, L.-L.C., Dillard, B.D., Liu, Z.-J., Bridger, S., Eneh, J.C., Hopkins, R.C., Jenney Jr, F.E., Lee, H.-S., Li, T., Poole II, F.L., Shah, C., Sugar, F.J., Adams, M.W.W., Arendall III, W.B., Richardson, J.S., Richardson, D.C., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.246
R-Value Work: 0.200
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

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

Literature

Conserved hypothetical protein from Pyrococcus furiosus Pfu-403030-001

Chen, L., Tempel, W., Habel, J., Zhou, W., Nguyen, D., Chang, S.-H., Lee, D., Kelley, L.-L.C., Dillard, B.D., Liu, Z.-J., Bridger, S., Eneh, J.C., Hopkins, R.C., Jenney Jr, F.E., Lee, H.-S., Li, T., Poole II, F.L., Shah, C., Sugar, F.J., Adams, M.W.W., Arendall III, W.B., Richardson, J.S., Richardson, D.C., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics

To be published.

Macromolecule Content

Total Structure Weight: 127.06 kDa
Atom Count: 7,822
Modelled Residue Count: 1,008
Deposited Residue Count: 1,104
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
oxetanocin-like protein	A, B, C, D, E A, B, C, D, E, F	184	Pyrococcus furiosus	Mutation(s): 0
UniProt
Find proteins for Q8U3R1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U3R1 Go to UniProtKB: Q8U3R1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8U3R1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain Y [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain Y [auth E]	CA [auth F] G [auth A] M [auth B] R [auth C] T [auth D] CA [auth F], G [auth A], M [auth B], R [auth C], T [auth D], Y [auth E]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain G [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain G [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain Y [auth E]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth E] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E]	AA [auth E] BA [auth E] DA [auth F] EA [auth F] H [auth A] AA [auth E], BA [auth E], DA [auth F], EA [auth F], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], S [auth C], U [auth D], V [auth D], W [auth D], X [auth D], Z [auth E]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] 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 U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] 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 U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.246
R-Value Work: 0.200
R-Value Observed: 0.201
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.073	α = 90
b = 111.335	β = 90
c = 125.984	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
ARP/wARP	model building
MolProbity	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-12-28

Deposition Author(s):

Southeast Collaboratory for Structural Genomics (SECSG)

Revision History (Full details and data files)

Version 1.0: 2004-12-28
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations