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- PDB-4qjp: Crystal structure of human carbonic anhydrase isozyme XIII with i... -

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Basic information

Entry
Database: PDB / ID: 4qjp
TitleCrystal structure of human carbonic anhydrase isozyme XIII with inhibitor
ComponentsCarbonic anhydrase 13
KeywordsLYASE/LYASE INHIBITOR / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / myelin sheath / intracellular membrane-bounded organelle / zinc ion binding / cytosol / cytoplasm
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
CITRIC ACID / DI(HYDROXYETHYL)ETHER / Chem-V1F / Carbonic anhydrase 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å
AuthorsManakova, E. / Smirnov, A. / Grazulis, S.
CitationJournal: Chemmedchem / Year: 2015
Title: Functionalization of Fluorinated Benzenesulfonamides and Their Inhibitory Properties toward Carbonic Anhydrases
Authors: Dudutiene, V. / Zubriene, A. / Smirnov, A. / Timm, D.D. / Smirnoviene, J. / Kazokaite, J. / Michailoviene, V. / Zaksauskas, A. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionJun 4, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.version
Revision 1.2Nov 8, 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_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_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_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
B: Carbonic anhydrase 13
A: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,87312
Polymers59,2272
Non-polymers1,64610
Water8,701483
1
B: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3315
Polymers29,6131
Non-polymers7184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5427
Polymers29,6131
Non-polymers9286
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.043, 57.544, 159.521
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Carbonic anhydrase 13 / Carbonate dehydratase XIII / Carbonic anhydrase XIII / CA-XIII


Mass: 29613.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA13 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N1Q1, carbonic anhydrase

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Non-polymers , 6 types, 493 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-V1F / 3-(benzylamino)-2,5,6-trifluoro-4-[(2-phenylethyl)sulfonyl]benzenesulfonamide


Mass: 484.512 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H19F3N2O4S2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.14 Å3/Da / Density % sol: 42.2 % / Mosaicity: 0.06 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M sodium citrate (pH 5.5), 0.1M sodium acetate (pH 4.5), 26% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.826606 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2012
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: 1.62→159.521 Å / Num. obs: 65652 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 19.076 Å2 / Rsym value: 0.038 / Net I/σ(I): 26.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.62-1.715.10.1740.1415.34383286350.070.170.1418.190
1.71-1.816.90.1280.1076.86250890850.050.130.10713.2100
1.81-1.946.60.0920.0768.95686985550.040.090.07617.9100
1.94-2.096.70.0680.05711.35355179600.030.070.05724100
2.09-2.296.80.0570.04813.15016373980.020.060.04829.4100
2.29-2.566.60.050.04114.54387666730.020.050.04133.8100
2.56-2.966.80.0440.03715.84048259580.020.040.03739100
2.96-3.626.60.0380.03217.23344150670.010.040.03243.9100
3.62-5.126.50.0360.03117.92581039880.010.040.03146.8100
5.12-159.526.20.040.033111438623330.020.040.03345.2100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.006data extraction
HKL-2000data collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NNO

2nno


Resolution: 1.62→54.13 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.177 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.876 / SU R Cruickshank DPI: 0.099 / SU Rfree: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.205 6556 10 %RANDOM
Rwork0.168 ---
all0.172 65569 --
obs0.172 65569 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.56 Å2 / Biso mean: 21.005 Å2 / Biso min: 8.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.65 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.62→54.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 102 483 4693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.024473
X-RAY DIFFRACTIONr_angle_refined_deg2.4411.9676113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8925545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98124.293205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46515703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2861520
X-RAY DIFFRACTIONr_chiral_restr0.1830.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213506
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 374 -
Rwork0.216 3551 -
all-3925 -
obs--80.91 %

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