1CI0 | pdb_00001ci0

PNP OXIDASE FROM SACCHAROMYCES CEREVISIAE

PDB DOI: https://doi.org/10.2210/pdb1CI0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1999-04-06 Released: 1999-08-25
Deposition Author(s): Shi, W., Ostrov, D.A., Gerchman, S.E., Graziano, V., Kycia, H., Studier, B., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.274 (Depositor)
R-Value Work:
0.225 (Depositor), 0.234 (DCC)
R-Value Observed:
0.230 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1CI0

Ligand Structure Quality Assessment

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

Literature

The Structure of PNP Oxidase from S. Cerevisiae

Shi, W., Ostrov, D.A., Gerchman, S.E., Graziano, V., Kycia, H., Studier, B., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 54.81 kDa
Atom Count: 3,441
Modeled Residue Count: 409
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PNP OXIDASE)	A, B	228	Saccharomyces cerevisiae	Mutation(s): 0 EC: 1.4.3.5
UniProt
Find proteins for P38075 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38075 Go to UniProtKB: P38075
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38075
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.274 (Depositor)
R-Value Work: 0.225 (Depositor), 0.234 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.97	α = 90
b = 74.97	β = 90
c = 157.14	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 1999-08-25

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 1999-08-25
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-02-03
Changes: Derived calculations, Structure summary
Version 1.4: 2023-12-27
Changes: Data collection, Database references

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.