5UBA | pdb_00005uba

Human RNA Pseudouridylate Synthase Domain Containing 4

• PDB DOI: https://doi.org/10.2210/pdb5UBA/pdb

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


• Deposited: 2016-12-20 Released: 2017-02-22 
• Deposition Author(s): DONG, A., ZENG, H., TEMPEL, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.212 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

The Crystal Structure of Human Pseudouridylate Synthase Domain Containing 4. To be published

ZENG, H., DONG, A., TEMPEL, W., 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: 33.62 kDa 
• Atom Count: 2,349 
• Modeled Residue Count: 262 
• Deposited Residue Count: 295 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA pseudouridylate synthase domain-containing protein 4	A	295	Homo sapiens	Mutation(s): 0  Gene Names: RPUSD4 EC: 5.4.99
UniProt & NIH Common Fund Data Resources
Find proteins for Q96CM3 (Homo sapiens) Explore Q96CM3  Go to UniProtKB:  Q96CM3
PHAROS:  Q96CM3 GTEx:  ENSG00000165526

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNX	F [auth A], G [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.212 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35UBA

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.189	α = 90
b = 54.189	β = 90
c = 105.349	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-22 
Deposition Author(s): DONG, A., ZENG, H., TEMPEL, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2017-02-22
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2018-04-18
  Changes: Data collection
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description