1T5Y | pdb_00001t5y

Crystal Structure of Northeast Structural Genomics Consortium Target HR2118: A Human Homolog of Saccharomyces cerevisiae Nip7p

PDB DOI: https://doi.org/10.2210/pdb1T5Y/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-05-05 Released: 2004-06-01
Deposition Author(s): Kuzin, A.P., Chen, Y., Forouhar, F., Acton, T.B., Shastry, R., Ma, L.-C., Cooper, B., Xiao, R., Montelione, G., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.294 (Depositor), 0.300 (DCC)
R-Value Work:
0.213 (Depositor), 0.222 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Northeast Structural Genomics Consortium Target HR2118: A Human Homolog of Saccharomyces cerevisiae Nip7p

Kuzin, A.P., Chen, Y., Forouhar, F., Acton, T.B., Shastry, R., Ma, L.-C., Cooper, B., Xiao, R., Montelione, G., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 22.02 kDa
Atom Count: 1,400
Modelled Residue Count: 170
Deposited Residue Count: 190
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SACCHAROMYCES CEREVISIAE Nip7p HOMOLOG	A	190	Homo sapiens	Mutation(s): 5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y221 (Homo sapiens) Explore Q9Y221 Go to UniProtKB: Q9Y221
PHAROS: Q9Y221 GTEx: ENSG00000132603
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y221
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.294 (Depositor), 0.300 (DCC)
R-Value Work: 0.213 (Depositor), 0.222 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.03	α = 90
b = 58.03	β = 90
c = 132.69	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-06-01

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2004-06-01
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: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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.