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- PDB-4ww8: Crystal structure of human carbonic anhydrase isozyme XII with 4-... -

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Basic information

Entry
Database: PDB / ID: 4ww8
TitleCrystal structure of human carbonic anhydrase isozyme XII with 4-Propylthiobenzenesulfonamide
ComponentsCarbonic anhydrase 12
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor comple
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
4-(propylsulfanyl)benzenesulfonamide / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Biophys.Chem. / Year: 2015
Title: Intrinsic thermodynamics of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamide binding to carbonic anhydrases by isothermal titration calorimetry.
Authors: Zubriene, A. / Smirnoviene, J. / Smirnov, A. / Morkunaite, V. / Michailoviene, V. / Jachno, J. / Juozapaitiene, V. / Norvaisas, P. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionNov 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)121,66325
Polymers119,6694
Non-polymers1,99421
Water16,430912
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,98715
Polymers59,8352
Non-polymers1,15213
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)60,67610
Polymers59,8352
Non-polymers8428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.313, 74.260, 91.570
Angle α, β, γ (deg.)90.000, 108.660, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains two dimers:

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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 / Fragment: UNP residues 30-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O43570, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Mutation: 4-Propylthiobenzenesulfonamide / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Fragment: Zn / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-VD9 / 4-(propylsulfanyl)benzenesulfonamide


Mass: 231.335 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13NO2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 912 / 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: 2.08 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystallization buffer: 0.1M ammonium citrate (pH 7.0), 0.2M ammonium sulfate and 30% PEG4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.826606 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826606 Å / Relative weight: 1
ReflectionResolution: 1.42→74.26 Å / Num. all: 176873 / Num. obs: 176873 / % possible obs: 95.8 % / Redundancy: 6.7 % / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Rsym value: 0.054 / Net I/av σ(I): 5.314 / Net I/σ(I): 16.7 / Num. measured all: 1192219
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
1.42-1.55.60.4530.372118275210900.190.450.3713.979
1.5-1.596.90.3190.272.7171340250060.120.320.27698.2
1.59-1.76.90.2090.1764.2161966236160.080.210.1768.398.6
1.7-1.836.90.1350.1126.4151777219700.050.140.11211.898.8
1.83-2.016.80.0880.0729.4138563202420.030.090.07216.998.8
2.01-2.256.80.0650.05311.8124324183230.030.060.05322.598.8
2.25-2.5970.0550.04512.9113745162830.020.050.04526.999.2
2.59-3.187.10.0480.0412.797329137290.020.050.0432.298.7
3.18-4.4970.0460.0411.874699106810.020.050.0438.299
4.49-74.266.80.0580.057.74020159330.020.060.0537.498.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PDB_EXTRACT3.006data extraction
SCALAdata scaling
REFMAC5.6.0117refinement
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JD0

1jd0


Resolution: 1.42→56.42 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.178 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.854 / SU R Cruickshank DPI: 0.072 / SU Rfree: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.205 17544 9.9 %RANDOM
Rwork0.172 159303 --
obs0.175 176847 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 78.64 Å2 / Biso mean: 18.976 Å2 / Biso min: 6.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20.24 Å2
2--0.31 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.42→56.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8380 0 112 912 9404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.028951
X-RAY DIFFRACTIONr_angle_refined_deg2.271.9512216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0351103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78424.7434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.229151377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.091528
X-RAY DIFFRACTIONr_chiral_restr0.1730.21276
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0217077
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 852 -
Rwork0.237 7938 -
all-8790 -
obs--64.39 %

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