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- PDB-1v9i: Crystal Structure Analysis of the site specific mutant (Q253C) of... -

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Basic information

Entry
Database: PDB / ID: 1v9i
TitleCrystal Structure Analysis of the site specific mutant (Q253C) of bovine carbonic anhydrase II
ComponentsCarbonic anhydrase II
KeywordsLYASE / BETA SHEET / ZINC METALLOENZYME
Function / homology
Function and homology information


positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / angiotensin-activated signaling pathway / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / one-carbon metabolic process ...positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / angiotensin-activated signaling pathway / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / one-carbon metabolic process / apical part of cell / zinc ion binding / plasma membrane / 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 2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSaito, R. / Sato, T. / Ikai, A. / Tanaka, N.
CitationJournal: To be Published
Title: Crystal Structure Analysis of the site specific mutant (Q253C) of bovine carbonic anhydrase II
Authors: Saito, R. / Sato, T. / Ikai, A. / Tanaka, N.
History
DepositionJan 26, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Carbonic anhydrase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3212
Polymers29,2561
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.100, 73.100, 116.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Carbonic anhydrase II / Carbonate dehydratase II / CA-II


Mass: 29255.912 Da / Num. of mol.: 1 / Mutation: Q253C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell: ERYTHROCYTES / Plasmid: pRSETB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PRSETB / References: UniProt: P00921, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 277 K / Method: small tubes / pH: 7.5
Details: 50mM Tris-HCl, 3mM NaN3, 2.3M Ammonium Sulfate, pH 7.5, SMALL TUBES, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.95→20 Å / Num. obs: 7798 / % possible obs: 99.2 % / Biso Wilson estimate: 0.9 Å2 / Rsym value: 0.075

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→20 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 945099.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.346 799 10.2 %RANDOM
Rwork0.247 ---
all-7806 --
obs-7798 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.5308 Å2 / ksol: 0.403137 e/Å3
Displacement parametersBiso mean: 61.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.08 Å212.38 Å20 Å2
2--8.08 Å20 Å2
3----16.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 1 0 2069
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it8.141.5
X-RAY DIFFRACTIONc_mcangle_it12.612
X-RAY DIFFRACTIONc_scbond_it9.782
X-RAY DIFFRACTIONc_scangle_it13.982.5
LS refinement shellResolution: 2.95→3.13 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 136 11.2 %
Rwork0.308 1078 -
obs--93.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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