4FU3 | pdb_00004fu3

CID of human RPRD1B

PDB DOI: https://doi.org/10.2210/pdb4FU3/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2012-06-28 Released: 2012-08-29
Deposition Author(s): Ni, Z., Xu, C., Tempel, W., El Bakkouri, M., Loppnau, P., Guo, X., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Greenblatt, J.F., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.259 (Depositor), 0.278 (DCC)
R-Value Work:
0.209 (Depositor), 0.223 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

CID of human RPRD1B

Ni, Z., Xu, C., Tempel, W., El Bakkouri, M., Loppnau, P., Guo, X., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Greenblatt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 31.3 kDa
Atom Count: 2,138
Modeled Residue Count: 256
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulation of nuclear pre-mRNA domain-containing protein 1B	A, B	135	Homo sapiens	Mutation(s): 0 Gene Names: RPRD1B, C20orf77, CREPT
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQG5 (Homo sapiens) Explore Q9NQG5 Go to UniProtKB: Q9NQG5
PHAROS: Q9NQG5 GTEx: ENSG00000101413
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NQG5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	C [auth A], D [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.259 (Depositor), 0.278 (DCC)
R-Value Work: 0.209 (Depositor), 0.223 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.752	α = 90
b = 79.784	β = 90
c = 108.666	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
BUSTER	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-08-29

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2012-08-29
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary