2P12 | pdb_00002p12

Crystal structure of protein of unknown function DUF402 from Rhodococcus sp. RHA1

• PDB DOI: https://doi.org/10.2210/pdb2P12/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Rhodococcus jostii RHA1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-03-01 Released: 2007-04-03 
• Deposition Author(s): Kim, Y., Evdokimova, E., Kudritska, M., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.216 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.171 (Depositor) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

The crystal structure of the protein of uncharacterized function, DUF402 from Rhodococcus sp. RHA1

Kim, Y., Evdokimova, E., Kudritska, M., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 40.92 kDa 
• Atom Count: 3,493 
• Modeled Residue Count: 331 
• Deposited Residue Count: 352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein DUF402	A, B	176	Rhodococcus jostii RHA1	Mutation(s): 4  Gene Names: RHA1_ro00977
UniProt
Find proteins for Q0SI31 (Rhodococcus jostii (strain RHA1)) Explore Q0SI31  Go to UniProtKB:  Q0SI31

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	C [auth A], E [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.216 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.171 (Depositor) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.203	α = 90
b = 38.98	β = 107.69
c = 70.721	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXCD	phasing
SHELXD	phasing
MLPHARE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-03 
Deposition Author(s): Kim, Y., Evdokimova, E., Kudritska, M., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-04-03
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary