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- PDB-4q0l: Crystal structure of catalytic domain of human carbonic anhydrase... -

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Basic information

Entry
Database: PDB / ID: 4q0l
TitleCrystal structure of catalytic domain of human carbonic anhydrase isozyme XII with inhibitor
ComponentsCarbonic anhydrase 12
KeywordsLYASE/LYASE INHIBITOR / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor comple / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


chloride ion homeostasis / estrous cycle / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / basolateral plasma membrane / apical plasma membrane / zinc ion binding / membrane / plasma membrane
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
Chem-V14 / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Discovery and characterization of novel selective inhibitors of carbonic anhydrase IX.
Authors: Dudutiene, V. / Matuliene, J. / Smirnov, A. / Timm, D.D. / Zubriene, A. / Baranauskiene, L. / Morkunaite, V. / Smirnoviene, J. / Michailoviene, V. / Juozapaitiene, V. / Mickeviciute, A. / ...Authors: Dudutiene, V. / Matuliene, J. / Smirnov, A. / Timm, D.D. / Zubriene, A. / Baranauskiene, L. / Morkunaite, V. / Smirnoviene, J. / Michailoviene, V. / Juozapaitiene, V. / Mickeviciute, A. / Kazokaite, J. / Baksyte, S. / Kasiliauskaite, A. / Jachno, J. / Revuckiene, J. / Kisonaite, M. / Pilipuityte, V. / Ivanauskaite, E. / Milinaviciute, G. / Smirnovas, V. / Petrikaite, V. / Kairys, V. / Petrauskas, V. / Norvaisas, P. / Linge, D. / Gibieza, P. / Capkauskaite, E. / Zaksauskas, A. / Kazlauskas, E. / Manakova, E. / Grazulis, S. / Ladbury, J.E. / Matulis, D.
History
DepositionApr 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
C: Carbonic anhydrase 12
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,70912
Polymers119,6694
Non-polymers2,0408
Water5,765320
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8546
Polymers59,8352
Non-polymers1,0204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Carbonic anhydrase 12
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8546
Polymers59,8352
Non-polymers1,0204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4273
Polymers29,9171
Non-polymers5102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4273
Polymers29,9171
Non-polymers5102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4273
Polymers29,9171
Non-polymers5102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4273
Polymers29,9171
Non-polymers5102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.520, 75.211, 77.888
Angle α, β, γ (deg.)109.420, 101.600, 107.950
Int Tables number1
Space group name H-MP1
DetailsThe asymmetric unit contains two dimers: first dimer (A, B chain) and second dimer (C, D chain).

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Components

#1: Protein
Carbonic anhydrase 12 / / Carbonate dehydratase XII / Carbonic anhydrase XII / CA-XII / Tumor antigen HOM-RCC-3.1.3


Mass: 29917.318 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O43570, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-V14 / 3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide


Mass: 444.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H23F3N2O5S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 1.92 Å3/Da / Density % sol: 35.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Crystallization buffer: 0.1M ammonium citrate with pH 5.0 and 18% of PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 15, 2012
RadiationMonochromator: VARIMAX-HF MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→22.11 Å / Num. obs: 44882 / % possible obs: 74.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 23.407 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.1130.2692.61710357300.26964.9
2.11-2.2430.1923.61699956390.19268
2.24-2.3930.1494.61587753300.14968.3
2.39-2.582.90.1096.11488451680.10970.6
2.58-2.832.80.0897.21382649230.08974
2.83-3.162.80.0736.21364649480.07381.4
3.16-3.652.90.0569.91341145510.05685.6
3.65-4.473.10.04711.51207539290.04786.9
4.47-6.323.10.04611.2941230420.04687
6.32-22.1130.0467.4492516220.04685.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
MOSFLMdata reduction
SCALA3.2.19data scaling
PDB_EXTRACT3.006data extraction
MOLREPphasing
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 1JD0

1jd0


Resolution: 2→22.09 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.327 / WRfactor Rwork: 0.266 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.603 / SU R Cruickshank DPI: 0.824 / SU Rfree: 0.352 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.824 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.328 4525 10.1 %RANDOM
Rwork0.264 ---
all0.27 44876 --
obs0.27 44876 74.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.97 Å2 / Biso mean: 20.194 Å2 / Biso min: 5.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20.2 Å20.57 Å2
2--0.26 Å20.67 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 2→22.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8372 0 116 320 8808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.028836
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.96112064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.30651053
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.87724.624439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.283151367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5161532
X-RAY DIFFRACTIONr_chiral_restr0.1160.21262
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216916
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 288 -
Rwork0.366 2458 -
all-2746 -
obs--61.93 %

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