3D0F | pdb_00003d0f

Structure of the BIG_1156.2 domain of putative penicillin-binding protein MrcA from Nitrosomonas europaea ATCC 19718

• PDB DOI: https://doi.org/10.2210/pdb3D0F/pdb

• Classification: TRANSFERASE
• Organism(s): Nitrosomonas europaea ATCC 19718
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-01 Released: 2008-07-01 
• Deposition Author(s): Cuff, M.E., Mulligan, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.217 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

Structure of the BIG_1156.2 domain of putative penicillin-binding protein MrcA from Nitrosomonas europaea ATCC 19718.

Cuff, M.E., Mulligan, R., Clancy, S., 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: 23.59 kDa 
• Atom Count: 2,109 
• Modeled Residue Count: 210 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding 1 transmembrane protein MrcA	A, B	106	Nitrosomonas europaea ATCC 19718	Mutation(s): 0  Gene Names: mrcA, NE2317 EC: 2.4.2 (PDB Primary Data), 2.4.99.28 (UniProt), 3.4.16.4 (UniProt)
UniProt
Find proteins for Q81ZZ3 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q81ZZ3  Go to UniProtKB:  Q81ZZ3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.64 Å
• R-Value Free:  0.217 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.206	α = 90
b = 52.219	β = 107.87
c = 56.86	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-01 
Deposition Author(s): Cuff, M.E., Mulligan, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-07-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary