3LAG | pdb_00003lag

The crystal structure of a functionally unknown protein RPA4178 from Rhodopseudomonas palustris CGA009

• PDB DOI: https://doi.org/10.2210/pdb3LAG/pdb
• Entry: 3LAG supersedes: 2OZI

• Classification: structural genomics, unknown function
• Organism(s): Rhodopseudomonas palustris CGA009
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-01-06 Released: 2010-01-19 
• Deposition Author(s): Tan, K., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

The crystal structure of a functionally unknown protein RPA4178 from Rhodopseudomonas palustris CGA009

Tan, K., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, 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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.91 kDa 
• Atom Count: 1,956 
• Modeled Residue Count: 193 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein RPA4178	A, B	98	Rhodopseudomonas palustris CGA009	Mutation(s): 0  Gene Names: PA4178
UniProt
Find proteins for Q6N272 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N272  Go to UniProtKB:  Q6N272

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth A], F [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
FMT	E [auth A], G [auth B], H [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 1.15 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.871	α = 90
b = 59.243	β = 90
c = 65.38	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-19 
Deposition Author(s): Tan, K., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 2OZI

Revision History  

• Version 1.0: 2010-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary