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- PDB-6g98: Three dimensional structure of human carbonic anhydrase IX in com... -

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Basic information

Entry
Database: PDB / ID: 6g98
TitleThree dimensional structure of human carbonic anhydrase IX in complex with sulfonamide
ComponentsCarbonic anhydrase 9
KeywordsLYASE
Function / homology
Function and homology information


Regulation of gene expression by Hypoxia-inducible Factor / response to testosterone / microvillus membrane / secretion / molecular function activator activity / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / basolateral plasma membrane ...Regulation of gene expression by Hypoxia-inducible Factor / response to testosterone / microvillus membrane / secretion / molecular function activator activity / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / basolateral plasma membrane / response to hypoxia / response to xenobiotic stimulus / nucleolus / 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-ER5 / Carbonic anhydrase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsLeitans, J. / Tars, K.
CitationJournal: Oncotarget / Year: 2018
Title: Novel fluorinated carbonic anhydrase IX inhibitors reduce hypoxia-induced acidification and clonogenic survival of cancer cells.
Authors: Kazokaite, J. / Niemans, R. / Dudutiene, V. / Becker, H.M. / Leitans, J. / Zubriene, A. / Baranauskiene, L. / Gondi, G. / Zeidler, R. / Matuliene, J. / Tars, K. / Yaromina, A. / Lambin, P. / ...Authors: Kazokaite, J. / Niemans, R. / Dudutiene, V. / Becker, H.M. / Leitans, J. / Zubriene, A. / Baranauskiene, L. / Gondi, G. / Zeidler, R. / Matuliene, J. / Tars, K. / Yaromina, A. / Lambin, P. / Dubois, L.J. / Matulis, D.
History
DepositionApr 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 9
B: Carbonic anhydrase 9
C: Carbonic anhydrase 9
D: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,24312
Polymers112,6914
Non-polymers2,5528
Water7,602422
1
A: Carbonic anhydrase 9
B: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6226
Polymers56,3452
Non-polymers1,2764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-9 kcal/mol
Surface area20260 Å2
MethodPISA
2
C: Carbonic anhydrase 9
D: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6226
Polymers56,3452
Non-polymers1,2764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-10 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.390, 152.390, 171.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Carbonic anhydrase 9 / Carbonate dehydratase IX / Carbonic anhydrase IX / CAIX / Membrane antigen MN / P54/58N / Renal ...Carbonate dehydratase IX / Carbonic anhydrase IX / CAIX / Membrane antigen MN / P54/58N / Renal cell carcinoma-associated antigen G250 / RCC-associated antigen G250 / pMW1


Mass: 28172.684 Da / Num. of mol.: 4 / Mutation: C42S
Source method: isolated from a genetically manipulated source
Details: A, B, C, D chains are identical. / Source: (gene. exp.) Homo sapiens (human) / Gene: CA9, G250, MN / Production host: Komagataella pastoris (fungus) / References: UniProt: Q16790, 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-ER5 / 4-[2-[3-(cyclododecylamino)-2,5,6-tris(fluoranyl)-4-sulfamoyl-phenyl]sulfanylethyl]benzoic acid


Mass: 572.703 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H35F3N2O4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.43 Å3/Da / Density % sol: 64.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.0 M DI-AMMONIUM HYDROGEN PHOSPHATE, 0.1 M SODIUM ACETATE PH 4.5, PROTEIN 10 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2018
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.47→76.19 Å / Num. obs: 53252 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.166 / Net I/σ(I): 7.7
Reflection shellResolution: 2.47→2.6 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.811 / Mean I/σ(I) obs: 2 / Num. unique obs: 7751 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FL4

5fl4


Resolution: 2.47→76.19 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.097 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.209 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20944 2703 5.1 %RANDOM
Rwork0.1691 ---
obs0.17122 50547 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.829 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.21 Å2-0 Å2
2--0.43 Å2-0 Å2
3----1.38 Å2
Refinement stepCycle: 1 / Resolution: 2.47→76.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7397 0 156 422 7975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197748
X-RAY DIFFRACTIONr_bond_other_d0.0020.027079
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.99410545
X-RAY DIFFRACTIONr_angle_other_deg0.943316423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0915942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97923.246345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.143151139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3091564
X-RAY DIFFRACTIONr_chiral_restr0.0770.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218553
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021563
X-RAY DIFFRACTIONr_mcbond_it2.2333.8963828
X-RAY DIFFRACTIONr_mcbond_other2.2273.8953827
X-RAY DIFFRACTIONr_mcangle_it3.6815.8284750
X-RAY DIFFRACTIONr_mcangle_other3.6825.8294751
X-RAY DIFFRACTIONr_scbond_it2.7344.2443920
X-RAY DIFFRACTIONr_scbond_other2.7344.2443921
X-RAY DIFFRACTIONr_scangle_other4.5486.2515796
X-RAY DIFFRACTIONr_long_range_B_refined6.83945.4238067
X-RAY DIFFRACTIONr_long_range_B_other6.81745.317999
LS refinement shellResolution: 2.47→2.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 190 -
Rwork0.285 3768 -
obs--99.4 %

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