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- PDB-3uyq: HCA 3 -

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Basic information

Entry
Database: PDB / ID: 3uyq
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 / 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: 1.7 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
SupersessionDec 21, 2011ID: 2HFX
Revision 1.0Dec 21, 2011Provider: 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)29,6562
Polymers29,5901
Non-polymers651
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.77, 50.78, 117.90
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: 29590.312 Da / Num. of mol.: 1 / Mutation: V31I, K64H, C182S, C188S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA3, hca3 / 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.: 304 / 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: 2.11 Å3/Da / Density % sol: 41.78 %
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 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 28430 / Num. obs: 27406 / % possible obs: 96.4 %
Reflection shellResolution: 1.7→1.76 Å / % possible all: 89

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Processing

Software
NameClassification
CrystalCleardata collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / Cross valid method: random / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.219 2666 throughout
Rwork0.205 --
all-28430 -
obs-27406 -
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 0 1 304 2387

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