5TF2 | pdb_00005tf2

CRYSTAL STRUCTURE OF THE WD40 DOMAIN OF THE HUMAN PROLACTIN REGULATORY ELEMENT-BINDING PROTEIN

PDB DOI: https://doi.org/10.2210/pdb5TF2/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2016-09-23 Released: 2016-11-23
Deposition Author(s): Walker, J.R., Zhang, Q., Dong, A., Wernimont, A., Li, Y., He, H., Tempel, W., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Chen, Z., Tong, Y., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.214 (Depositor), 0.217 (DCC)
R-Value Work:
0.189 (Depositor), 0.191 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

CRYSTAL STRUCTURE OF THE WD40 DOMAIN OF THE HUMAN PROLACTIN REGULATORY ELEMENT-BINDING PROTEIN (CASP target)

Walker, J.R., Zhang, Q., Dong, A., Wernimont, A., Li, Y., He, H., Tempel, W., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Chen, Z., Tong, Y., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 44.68 kDa
Atom Count: 2,564
Modeled Residue Count: 338
Deposited Residue Count: 407
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolactin regulatory element-binding protein	A	407	Homo sapiens	Mutation(s): 0 Gene Names: PREB, SEC12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCU5 (Homo sapiens) Explore Q9HCU5 Go to UniProtKB: Q9HCU5
PHAROS: Q9HCU5 GTEx: ENSG00000138073
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HCU5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.214 (Depositor), 0.217 (DCC)
R-Value Work: 0.189 (Depositor), 0.191 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.708	α = 90
b = 160.708	β = 90
c = 83.014	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
BALBES	phasing
BUCCANEER	model building

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-11-23

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2016-11-23
Type: Initial release
Version 1.1: 2017-08-16
Changes: Source and taxonomy
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description