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- PDB-4wup: Crystal structure of human carbonic anhydrase isozyme I with 4-[(... -

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Basic information

Entry
Database: PDB / ID: 4wup
TitleCrystal structure of human carbonic anhydrase isozyme I with 4-[(2-Hydroxyethyl)thio]benzenesulfonamide
ComponentsCarbonic anhydrase 1
KeywordsLYASE / drug design / 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 / 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
4-[(2-hydroxyethyl)sulfanyl]benzenesulfonamide / ACETATE ION / 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
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 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,4338
Polymers57,6702
Non-polymers7636
Water6,666370
1
A: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1934
Polymers28,8351
Non-polymers3583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2404
Polymers28,8351
Non-polymers4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.332, 71.284, 120.719
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

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Protein , 1 types, 2 molecules AB

#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: UNP residues 3-261
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

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Non-polymers , 5 types, 376 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Fragment: 4-[(2-Hydroxyethyl)thio]benzenesulfonamide / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-3UF / 4-[(2-hydroxyethyl)sulfanyl]benzenesulfonamide


Mass: 233.308 Da / Num. of mol.: 2 / Fragment: Zn / Source method: obtained synthetically / Formula: C8H11NO3S2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Fragment: ACETATE ION / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Fragment: DI(HYDROXYETHYL)ETHER / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.37 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystallization buffer: 0.1M TrisHCl (pH 8.5), 0.2M ammonium acetate and 24% of 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, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826606 Å / Relative weight: 1
ReflectionResolution: 1.75→71.284 Å / Num. all: 55864 / Num. obs: 55864 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 23.016 Å2 / Rpim(I) all: 0.025 / Rrim(I) all: 0.091 / Rsym value: 0.085 / Net I/av σ(I): 4.004 / Net I/σ(I): 16.6 / Num. measured all: 733336
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
1.75-1.8413.20.370.3452.110614780220.10.370.34516.3100
1.84-1.9613.20.2430.2283.110056275930.070.240.2288.799.9
1.96-2.0913.10.1680.1574.49428371920.050.170.15711.7100
2.09-2.2613.20.1290.125.38843067120.040.130.1214.6100
2.26-2.4712.90.1060.0996.37952561830.030.110.0991799.9
2.47-2.7713.30.0930.0876.87475756100.030.090.08720.599.9
2.77-3.213.40.0860.08176716149940.020.090.08125100
3.2-3.9113.10.080.0767.25577642450.020.080.07629.8100
3.91-5.53130.0740.077.24363933540.020.070.0731100
5.53-71.2811.80.0720.0685.92305619590.020.070.06828.299.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1cab
PDB Unreleased entry


Resolution: 1.75→60.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.196 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.836 / SU R Cruickshank DPI: 0.126 / SU Rfree: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 5608 10.1 %RANDOM
Rwork0.185 50159 --
obs0.189 55767 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 82 Å2 / Biso mean: 24.864 Å2 / Biso min: 10.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--1.12 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 1.75→60.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4023 0 41 370 4434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.024269
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.945820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0945531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49624.718195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87815662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.041514
X-RAY DIFFRACTIONr_chiral_restr0.1620.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213331
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 411 -
Rwork0.222 3618 -
all-4029 -
obs--99.8 %

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