5UQP | pdb_00005uqp

The crystal structure of cupin protein from Rhodococcus jostii RHA1

• PDB DOI: https://doi.org/10.2210/pdb5UQP/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Rhodococcus jostii RHA1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-08 Released: 2017-02-22 
• Deposition Author(s): Tan, K., Li, H., Clancy, S., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.200 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

The crystal structure of cupin protein from Rhodococcus jostii RHA1

Tan, K., Li, H., Clancy, S., Phillips Jr., G.N., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 28.09 kDa 
• Atom Count: 1,849 
• Modeled Residue Count: 222 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin	A, B	125	Rhodococcus jostii RHA1	Mutation(s): 0  Gene Names: RHA1_ro08652
UniProt
Find proteins for Q0RYE0 (Rhodococcus jostii (strain RHA1)) Explore Q0RYE0  Go to UniProtKB:  Q0RYE0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.200 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.448	α = 90
b = 139.448	β = 90
c = 80.075	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-02-22 
Deposition Author(s): Tan, K., Li, H., Clancy, S., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115586

Revision History  

• Version 1.0: 2017-02-22
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations