2R5R | pdb_00002r5r

The crystal structure of DUF198 from Nitrosomonas europaea ATCC 19718

• PDB DOI: https://doi.org/10.2210/pdb2R5R/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Nitrosomonas europaea ATCC 19718
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-09-04 Released: 2007-09-18 
• Deposition Author(s): Tan, K., Wu, R., Nocek, B., Bigelow, L., Patterson, S., Freeman, L., Bargassa, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 
  0.261 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Literature

The crystal structure of DUF198 from Nitrosomonas europaea ATCC 19718.

Tan, K., Wu, R., Nocek, B., Bigelow, L., Patterson, S., Freeman, L., Bargassa, M., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.37 kDa 
• Atom Count: 1,988 
• Modeled Residue Count: 246 
• Deposited Residue Count: 271 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0343 protein NE1163	A	271	Nitrosomonas europaea ATCC 19718	Mutation(s): 0  Gene Names: NE1163 EC: 3.5.4.16
UniProt
Find proteins for Q82VD1 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q82VD1  Go to UniProtKB:  Q82VD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
IMD	C [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

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: 3.05 Å
• R-Value Free:  0.261 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.705	α = 90
b = 118.705	β = 90
c = 113.21	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MLPHARE	phasing
DM	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-18 
Deposition Author(s): Tan, K., Wu, R., Nocek, B., Bigelow, L., Patterson, S., Freeman, L., Bargassa, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-09-18
  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