2VSP | pdb_00002vsp

Crystal structure of the fourth PDZ domain of PDZ domain-containing protein 1

PDB DOI: https://doi.org/10.2210/pdb2VSP/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-04-28 Released: 2009-03-03
Deposition Author(s): Yue, W.W., Shafqat, N., Pilka, E.S., Johansson, C., Murray, J.W., Elkins, J., Roos, A., Cooper, C., Phillips, C., Salah, E., von Delft, F., Doyle, D., Edwards, A., Wikstrom, M., Arrowsmith, C., Bountra, C., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.267 (Depositor), 0.262 (DCC)
R-Value Work:
0.215 (Depositor), 0.234 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the Fourth Pdz Domain of Pdz Domain-Containing Protein 1

Yue, W.W., Shafqat, N., Pilka, E.S., von Delft, F., Johansson, C., Elkins, J., Roos, A., Murray, J.W., Doyle, D., Edwards, A., Arrowsmith, C., Bountra, C., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 39.18 kDa
Atom Count: 2,466
Modeled Residue Count: 329
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PDZ DOMAIN-CONTAINING PROTEIN 1	A, B, C, D	91	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T2W1 (Homo sapiens) Explore Q5T2W1 Go to UniProtKB: Q5T2W1
PHAROS: Q5T2W1 GTEx: ENSG00000174827
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5T2W1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.267 (Depositor), 0.262 (DCC)
R-Value Work: 0.215 (Depositor), 0.234 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.327	α = 90
b = 99.327	β = 90
c = 97.114	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-03-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-03-03
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-01-24
Changes: Database references, Structure summary
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description