3TMJ | pdb_00003tmj

Joint X-ray/neutron structure of human carbonic anhydrase II at pH 7.8

• PDB DOI: https://doi.org/10.2210/pdb3TMJ/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-31 Released: 2011-11-09 
• Deposition Author(s): Fisher, Z.

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.294 (Depositor) 
• R-Value Work: 
  0.280 (Depositor) 

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• Method: X-RAY DIFFRACTION
• R-Value Free: 
  0.180 (DCC) 
• R-Value Work: 
  0.171 (DCC) 

Starting Model: experimental

Literature

Neutron Structure of Human Carbonic Anhydrase II: A Hydrogen-Bonded Water Network "Switch" Is Observed between pH 7.8 and 10.0.

Fisher, Z., Kovalevsky, A.Y., Mustyakimov, M., Silverman, D.N., McKenna, R., Langan, P.

(2011) Biochemistry 50: 9421-9423

• PubMed: 21988105 
• DOI: https://doi.org/10.1021/bi201487b
• Primary Citation Related Structures: 
  3TMJ


• PubMed Abstract: 
  

  The neutron structure of wild-type human carbonic anhydrase II at pH 7.8 has been determined to 2.0 Å resolution. Detailed analysis and comparison to the previously determined structure at pH 10.0 show important differences in the protonation of key catalytic residues in the active site as well as a rearrangement of the H-bonded water network. For the first time, a completed H-bonded network stretching from the Zn-bound solvent to the proton shuttling residue, His64, has been directly observed.

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Organizational Affiliation: 
• Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87544, United States. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 29.14 kDa 
• Atom Count: 2,256 
• Modeled Residue Count: 258 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	258	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.294 (Depositor) 
• R-Value Work:  0.280 (Depositor) 

• Method: X-RAY DIFFRACTION
• R-Value Free:  0.180 (DCC) 
• R-Value Work:  0.171 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.83	α = 90
b = 41.7	β = 104.58
c = 72.92	γ = 90

Software Package:

Software Name	Purpose
PCS	data collection
nCNS	refinement
d*TREK	data reduction
SCALA	data scaling
d*TREK	data scaling
nCNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-09 
Deposition Author(s): Fisher, Z.

Revision History  

• Version 1.0: 2011-11-09
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2018-04-25
  Changes: Data collection
• Version 1.3: 2018-06-13
  Changes: Data collection
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description