5VBB | pdb_00005vbb

Human RNA Pseudouridylate Synthase Domain Containing 1

• PDB DOI: https://doi.org/10.2210/pdb5VBB/pdb

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


• Deposited: 2017-03-29 Released: 2017-04-19 
• Deposition Author(s): DONG, A., ZENG, H., WALKER, J.R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.224 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Human RNA Pseudouridylate Synthase Domain Containing 1

ZENG, H., DONG, A., WALKER, J.R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.79 kDa 
• Atom Count: 2,026 
• Modeled Residue Count: 245 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA pseudouridylate synthase domain-containing protein 1	A	261	Homo sapiens	Mutation(s): 0  Gene Names: RPUSD1, C16orf40, RLUCL
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJJ7 (Homo sapiens) Explore Q9UJJ7  Go to UniProtKB:  Q9UJJ7
PHAROS:  Q9UJJ7 GTEx:  ENSG00000007376

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.224 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35VBB

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.2	α = 90
b = 92.44	β = 90
c = 88.89	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
BALBES	phasing
HKL-3000	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): DONG, A., ZENG, H., WALKER, J.R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary