2I14 | pdb_00002i14

Crystal structure of nicotinate-nucleotide pyrophosphorylase from Pyrococcus furiosus

PDB DOI: https://doi.org/10.2210/pdb2I14/pdb

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

Deposited: 2006-08-12 Released: 2006-10-10
Deposition Author(s): Shin, D.H., Kim, R., Kim, S.-H., Berkeley Structural Genomics Center (BSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.282 (Depositor), 0.284 (DCC)
R-Value Work:
0.247 (Depositor), 0.250 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of nicotinate-nucleotide pyrophosphorylase from Pyrococcus furiosus

Shin, D.H., Kim, R., Kim, S.-H., Pufan, R., Yokota, H.

To be published.

Macromolecule Content

Total Structure Weight: 265.74 kDa
Atom Count: 18,539
Modeled Residue Count: 2,334
Deposited Residue Count: 2,370
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinate-nucleotide pyrophosphorylase	A, B, C, D, E A, B, C, D, E, F	395	Pyrococcus furiosus	Mutation(s): 0 Gene Names: PF1904 EC: 6.3.4.21
UniProt
Find proteins for Q8TZS9 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8TZS9 Go to UniProtKB: Q8TZS9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TZS9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PCP Query on PCP Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain R [auth D] SDF format, chain X [auth F] SDF format, chain U [auth E] SDF format, chain O [auth C] SDF format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth D] MOL2 format, chain X [auth F] MOL2 format, chain U [auth E] MOL2 format, chain O [auth C] MOL2 format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth D] mmCIF format, chain X [auth F] mmCIF format, chain U [auth E] mmCIF format, chain O [auth C] mmCIF format, chain I [auth A]	I [auth A] L [auth B] O [auth C] R [auth D] U [auth E] I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE C₆ H₁₅ O₁₃ P₃ OICBXEWBKALHHB-MOJAZDJTSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain V [auth F] SDF format, chain W [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F] MOL2 format, chain W [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain V [auth F] mmCIF format, chain W [auth F]	G [auth A] H [auth A] J [auth B] K [auth B] M [auth C] G [auth A], H [auth A], J [auth B], K [auth B], M [auth C], N [auth C], P [auth D], Q [auth D], S [auth E], T [auth E], V [auth F], W [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.282 (Depositor), 0.284 (DCC)
R-Value Work: 0.247 (Depositor), 0.250 (DCC)
R-Value Observed: 0.247 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.481	α = 90
b = 111.481	β = 90
c = 178.263	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-10-10

Deposition Author(s):

Shin, D.H.

Kim, R.

Kim, S.-H.

Berkeley Structural Genomics Center (BSGC)

Revision History (Full details and data files)

Version 1.0: 2006-10-10
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description