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- PDB-1jv0: THE CRYSTAL STRUCTURE OF THE ZINC(II) ADDUCT OF THE CAI MICHIGAN ... -

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Basic information

Entry
Database: PDB / ID: 1jv0
TitleTHE CRYSTAL STRUCTURE OF THE ZINC(II) ADDUCT OF THE CAI MICHIGAN 1 VARIANT
ComponentsCARBONIC ANHYDRASE ICarbonic anhydrase
KeywordsLYASE / 10-STRANDED-BETA-SHEET
Function / homology
Function and homology information


hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen ...hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / extracellular exosome / zinc ion binding / cytosol
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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsBriganti, F. / Ferraroni, M. / Chegwidden, W.R. / Scozzafava, A. / Supuran, C.T. / Tilli, S.
Citation
Journal: Biochemistry / Year: 2002
Title: Crystal structure of a zinc-activated variant of human carbonic anhydrase I, CA I Michigan 1: evidence for a second zinc binding site involving arginine coordination
Authors: Ferraroni, M. / Tilli, S. / Briganti, F. / Chegwidden, W.R. / Supuran, C.T. / Wiebauer, K.E. / Tashian, R.E. / Scozzafava, A.
#1: Journal: Science / Year: 1962
Title: New genetically determined molecular form of erythrocite esterase in man
Authors: Shaw, C.R. / Syner, F.N. / Tashian, R.E.
#2: Journal: HUM.MUTAT. / Year: 1994
Title: Marked zinc activation of ester hydrolysis by a mutation, 67-HIS (CAT) To ARG (CGT), in the active site of human carbonic anhydrase I
Authors: Chegwidden, W.R. / Wagner, L.E. / Venta, P.J. / Bergenhem, N.C. / Yu, Y.S. / Tashian, R.E.
#3: Journal: GENE FAM.LSOZYME BULL. / Year: 1998
Title: Point mutation in the variant of human carbonic anhydrase isozyme I (CAI MICHIGAN) active site decreases affinity for aromatic sulfonamide inhibitors
Authors: Briganti, F. / Chegwidden, W.R. / Scozzafava, A. / Supuran, C.T. / Tashian, R.E. / Wiebauer, K.E.
History
DepositionAug 28, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE I
B: CARBONIC ANHYDRASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,21113
Polymers57,5882
Non-polymers62311
Water7,927440
1
A: CARBONIC ANHYDRASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0886
Polymers28,7941
Non-polymers2945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CARBONIC ANHYDRASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1237
Polymers28,7941
Non-polymers3296
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.681, 71.356, 120.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailstwo molecules in the asymmetric units related by a translation

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Components

#1: Protein CARBONIC ANHYDRASE I / Carbonic anhydrase / CA-I


Mass: 28794.035 Da / Num. of mol.: 2 / Mutation: H67R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PKK232-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00915, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.25 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 4000, LITIUM CHLORIDE, ETHYLENE GLICOL , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M12XHF / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 1000 / Detector: CCD / Date: Mar 21, 2001 / Details: GOBEL MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. all: 35578 / Num. obs: 35578 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.085 / Net I/σ(I): 8
Reflection shellResolution: 2→2.071 Å / Mean I/σ(I) obs: 2.18 / Rsym value: 0.277 / % possible all: 81.9

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Processing

Software
NameClassification
SAINTdata scaling
SAINTdata reduction
REFMACrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1J9W

1j9w


Resolution: 2→15 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1581 5.276 %RANDOM
Rwork0.197 ---
all-29964 --
obs-29964 --
Displacement parametersBiso mean: 27.8 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3981 0 17 440 4438
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d0.0420.05
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_mcbond_it1.5862
X-RAY DIFFRACTIONp_mcangle_it2.4263
X-RAY DIFFRACTIONp_scbond_it1.9452
X-RAY DIFFRACTIONp_scangle_it2.93
X-RAY DIFFRACTIONp_planar_d0.0810.05
X-RAY DIFFRACTIONp_special_tor015
X-RAY DIFFRACTIONp_planar_tor12.97
X-RAY DIFFRACTIONp_staggered_tor1615
X-RAY DIFFRACTIONp_transverse_tor29.120

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