3K63 | pdb_00003k63

X-ray structure of the PF04200 domain from Q9PRA0_UREPA protein of Ureaplasma parvum. NESG target UuR17a.

• PDB DOI: https://doi.org/10.2210/pdb3K63/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Ureaplasma parvum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-08 Released: 2009-10-20 
• Deposition Author(s): Vorobiev, S., Neely, H., Seetharaman, J., Lee, D., Ciccosanti, C., Mao, L., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.248 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

X-ray structure of the PF04200 domain from Q9PRA0_UREPA protein of Ureaplasma parvum.

Vorobiev, S., Neely, H., Seetharaman, J., Lee, D., Ciccosanti, C., Mao, L., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 14.88 kDa 
• Atom Count: 999 
• Modeled Residue Count: 120 
• Deposited Residue Count: 126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved hypothetical membrane lipoprotein	A	126	Ureaplasma parvum	Mutation(s): 0  Gene Names: UU045
UniProt
Find proteins for Q9PRA0 (Ureaplasma parvum serovar 3 (strain ATCC 700970)) Explore Q9PRA0  Go to UniProtKB:  Q9PRA0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.248 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.557	α = 90
b = 60.557	β = 90
c = 64.716	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELX	model building
RESOLVE	model building
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Vorobiev, S., Neely, H., Seetharaman, J., Lee, D., Ciccosanti, C., Mao, L., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary