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- PDB-6fe2: Three dimensional structure of human carbonic anhydrase IX -

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Basic information

Entry
Database: PDB / ID: 6fe2
TitleThree dimensional structure of human carbonic anhydrase IX
ComponentsCarbonic anhydrase 9
KeywordsLYASE
Function / homology
Function and homology information


Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / secretion / Reversible hydration of carbon dioxide / molecular function activator activity / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process ...Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / secretion / Reversible hydration of carbon dioxide / molecular function activator activity / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / 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
Carbonic anhydrase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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
DepositionDec 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)112,9528
Polymers112,6914
Non-polymers2624
Water13,745763
1
D: Carbonic anhydrase 9
hetero molecules

C: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4764
Polymers56,3452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-y-1/3,x-y+1/3,z+1/31
2
A: Carbonic anhydrase 9
B: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4764
Polymers56,3452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-83 kcal/mol
Surface area20650 Å2
MethodPISA
3
C: Carbonic anhydrase 9
hetero molecules

D: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4764
Polymers56,3452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_444-x+y-2/3,-x-1/3,z-1/31
Buried area1850 Å2
ΔGint-85 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.670, 152.670, 170.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-462-

HOH

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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
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 763 / 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: 3.42 Å3/Da / Density % sol: 64.04 %
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: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2016
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.87→31.7 Å / Num. obs: 121775 / % possible obs: 99.3 % / Redundancy: 2.7 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 9.9
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2 / Num. unique obs: 17762 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IAI

3iai


Resolution: 1.87→31.7 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.834 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19894 6280 5.2 %RANDOM
Rwork0.17193 ---
obs0.17337 115490 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.494 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.17 Å2-0 Å2
2--0.35 Å2-0 Å2
3----1.13 Å2
Refinement stepCycle: 1 / Resolution: 1.87→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7656 0 4 763 8423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197930
X-RAY DIFFRACTIONr_bond_other_d0.0020.027199
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.96710815
X-RAY DIFFRACTIONr_angle_other_deg0.901316701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.845992
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06523.175359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.923151158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7851565
X-RAY DIFFRACTIONr_chiral_restr0.0790.21179
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021628
X-RAY DIFFRACTIONr_mcbond_it2.0363.3483983
X-RAY DIFFRACTIONr_mcbond_other2.0353.3483982
X-RAY DIFFRACTIONr_mcangle_it3.1894.9964943
X-RAY DIFFRACTIONr_mcangle_other3.1884.9964944
X-RAY DIFFRACTIONr_scbond_it2.523.6263947
X-RAY DIFFRACTIONr_scbond_other2.5193.6253947
X-RAY DIFFRACTIONr_scangle_other4.0395.3465863
X-RAY DIFFRACTIONr_long_range_B_refined6.4740.8118562
X-RAY DIFFRACTIONr_long_range_B_other6.26340.1188369
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 438 -
Rwork0.274 8518 -
obs--99.04 %

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