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- PDB-1j9w: Solution Structure of the CAI Michigan 1 Variant -

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Basic information

Entry
Database: PDB / ID: 1j9w
TitleSolution Structure 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBriganti, F. / Ferraroni, M. / Chedwiggen, 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 erythrocyte 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
DepositionMay 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 26, 2014Group: Database references
Revision 1.4Feb 1, 2017Group: Structure summary
Revision 1.5Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.6Oct 27, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 1.7Aug 16, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,8436
Polymers57,5882
Non-polymers2554
Water5,783321
1
A: CARBONIC ANHYDRASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9223
Polymers28,7941
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CARBONIC ANHYDRASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9223
Polymers28,7941
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.875, 71.732, 120.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological assembly is a dimer generated by a translation

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Components

#1: Protein CARBONIC ANHYDRASE I / Carbonic anhydrase / CARBONATE DEHYDRATASE 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 321 / 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
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlenzyme1drop
210 mMTris sulfate1drop
325 %(w/v)PEG40001reservoir
40.4 M1reservoirLiCl
5100 mMTris-HCl1reservoir
610 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M12X / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 1000 / Detector: CCD / Date: May 26, 2000 / Details: mirrors
RadiationMonochromator: Gobel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 58715 / Num. obs: 58715 / % possible obs: 97.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 24.36 Å2 / Rsym value: 0.094 / Net I/σ(I): 7.8
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 1.5 / Num. unique all: 17135 / Rsym value: 0.244 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 17329 / Num. measured all: 58715 / Rmerge(I) obs: 0.094

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Processing

Software
NameClassification
SAINTdata scaling
SAINTdata reduction
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1czm

1czm


Resolution: 2.6→15 Å
Isotropic thermal model: isotropic, anisotropic for metal ions, sulfur atoms, choride ions
Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.311 877 5 %random
Rwork0.205 ---
all-15989 --
Displacement parametersBiso mean: 27.82 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 10 321 4305
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d0.040.05
X-RAY DIFFRACTIONp_bond_d0.0080.02
X-RAY DIFFRACTIONp_planar_d0.0790.05
X-RAY DIFFRACTIONp_planar_tor13.27
X-RAY DIFFRACTIONp_staggered_tor16.415
X-RAY DIFFRACTIONp_transverse_tor29.720
X-RAY DIFFRACTIONp_mcangle_it1.7953
X-RAY DIFFRACTIONp_mcbond_it1.032
X-RAY DIFFRACTIONp_scbond_it1.0872
X-RAY DIFFRACTIONp_scangle_it1.7933
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.046
X-RAY DIFFRACTIONp_planar_d0.093

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