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- PDB-4wuq: Crystal structure of human carbonic anhydrase isozyme I with 2,3,... -

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Basic information

Entry
Database: PDB / ID: 4wuq
TitleCrystal structure of human carbonic anhydrase isozyme I with 2,3,5,6-Tetrafluoro-4-piperidin-1-ylbenzenesulfonamide
ComponentsCarbonic anhydrase 1
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex
Function / homology
Function and homology information


hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase activity / cyanamide hydratase / 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 activity / cyanamide hydratase / 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 / extracellular exosome / zinc ion binding / cytoplasm / 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
Chem-3UG / DI(HYDROXYETHYL)ETHER / Carbonic anhydrase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsManakova, E. / Smirnov, A. / 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 3, 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

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Assembly

Deposited unit
A: Carbonic anhydrase 1
B: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5327
Polymers57,6702
Non-polymers8625
Water6,485360
1
A: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2133
Polymers28,8351
Non-polymers3782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3194
Polymers28,8351
Non-polymers4843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.601, 71.204, 119.935
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Carbonic anhydrase 1 / Carbonate dehydratase I / Carbonic anhydrase B / CAB / Carbonic anhydrase I / CA-I


Mass: 28835.105 Da / Num. of mol.: 2 / Fragment: human carbonic anhydrase I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00915, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Fragment: 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide
Mutation: ligandas / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-3UG / 2,3,5,6-tetrafluoro-4-(piperidin-1-yl)benzenesulfonamide


Mass: 312.284 Da / Num. of mol.: 2 / Fragment: Zn / Source method: obtained synthetically / Formula: C11H12F4N2O2S
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Fragment: ACETATE ION / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.36 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: Crystallization buffer: 0.1M TrisHCl (pH 8.5), 0.2M sodium acetate (pH 8.3), 28% of PEG3350.

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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: May 24, 2013
RadiationMonochromator: High Heat Load (HHL) Monochromator: Si 111; Large Offset Monochromator (LOM): Si 311, Si 511
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826606 Å / Relative weight: 1
ReflectionResolution: 1.75→119.935 Å / Num. all: 54897 / Num. obs: 54897 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 20.385 Å2 / Rpim(I) all: 0.021 / Rrim(I) all: 0.078 / Rsym value: 0.073 / Net I/av σ(I): 6.526 / Net I/σ(I): 21.4 / Num. measured all: 726651
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
1.75-1.8413.40.440.4111.610582479170.120.440.41117.3100
1.84-1.9613.40.2850.2672.410009474870.080.280.26710.3100
1.96-2.0913.20.1940.1813.69322870460.050.190.18113.7100
2.09-2.2613.30.140.1358726565740.040.140.1317.4100
2.26-2.47130.1060.0986.77863360650.030.110.09821.1100
2.47-2.7713.40.0850.0798.17402755190.020.090.07925.7100
2.77-3.213.60.0690.0649.76629648900.020.070.06432.8100
3.2-3.9113.20.0570.05310.95545841920.020.060.05341.699.9
3.91-5.5313.10.0450.04213.84304532790.010.050.04244.6100
5.53-119.9311.80.0480.0439.32278119280.010.050.04339.7100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.20data scaling
Cootmodel building
MOLREPphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CAB

1cab
PDB Unreleased entry


Resolution: 1.75→61.23 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.871 / SU R Cruickshank DPI: 0.119 / SU Rfree: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21 5591 10.2 %RANDOM
Rwork0.173 49229 --
obs0.176 54820 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 74.96 Å2 / Biso mean: 21.769 Å2 / Biso min: 8.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--1.56 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.75→61.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 49 360 4447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.024291
X-RAY DIFFRACTIONr_angle_refined_deg2.0991.9435861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2095537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.79824.691194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52515666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.521515
X-RAY DIFFRACTIONr_chiral_restr0.170.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213344
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 376 -
Rwork0.224 3631 -
all-4007 -
obs--99.93 %

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