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- PDB-3uyn: HCA 3 -

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Basic information

Entry
Database: PDB / ID: 3uyn
TitleHCA 3
ComponentsCarbonic anhydrase 3
KeywordsLYASE / PROTON SHUTTLE / HCA III / PROTON TRANSFER
Function / homology
Function and homology information


nickel cation binding / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / response to bacterium / one-carbon metabolic process / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase ...Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Roll / Alpha Beta
Similarity search - Domain/homology
Carbonic anhydrase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFisher, Z. / McKenna, R.
CitationJournal: Proteins / Year: 2007
Title: Structural and kinetic analysis of proton shuttle residues in the active site of human carbonic anhydrase III.
Authors: Elder, I. / Fisher, Z. / Laipis, P.J. / Tu, C. / McKenna, R. / Silverman, D.N.
History
DepositionDec 6, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 1, 2012ID: 2HFY
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6282
Polymers29,5621
Non-polymers651
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.198, 78.066, 43.383
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbonic anhydrase 3 / Carbonate dehydratase III / Carbonic anhydrase III / CA-III


Mass: 29562.301 Da / Num. of mol.: 1 / Mutation: V31I, R67H, C182S, C188S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA3 / Production host: Escherichia coli (E. coli) / References: UniProt: P07451, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.8
Details: 0.2 M AMMONIUM ACETATE 0.1 M SODIUM ACETATE 30% PEG 4K, PH 5.8, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 8839 / Num. obs: 8326 / % possible obs: 94.2 %
Reflection shellResolution: 2.6→2.69 Å / % possible all: 90.8

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Processing

Software
NameClassification
CrystalCleardata collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / Cross valid method: random / Stereochemistry target values: Engh & Huber
Details: THIS ENTRY SUPERSEDES 2HFY. THE COORDINATES IN 2HFY HAD BEEN CORRECTED FOR unassigned density in the active site AND THE CONFORMATION OF Zn-OORDINATING His residues. RE-REFINEMENT WAS NOT ...Details: THIS ENTRY SUPERSEDES 2HFY. THE COORDINATES IN 2HFY HAD BEEN CORRECTED FOR unassigned density in the active site AND THE CONFORMATION OF Zn-OORDINATING His residues. RE-REFINEMENT WAS NOT DONE AFTER CORRECTION. BETTER RFREE VALUES THAN RWORK IS NOTED FOR THIS ENTRY.
RfactorNum. reflectionSelection details
Rfree0.201 438 throughout
Rwork0.206 --
all-8839 -
obs-8326 -
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 1 53 2135

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