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- PDB-5dvx: Crystal structure of the catalytic-domain of human carbonic anhyd... -

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Basic information

Entry
Database: PDB / ID: 5dvx
TitleCrystal structure of the catalytic-domain of human carbonic anhydrase IX at 1.6 angstrom resolution
ComponentsCarbonic anhydrase 9
KeywordsLYASE / carbonic anhydrase IX / catalytic domain / water network
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: 1.598 Å
AuthorsMahon, B.P. / Socorro, L. / Driscoll, J.M. / McKenna, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA165284 United States
CitationJournal: Biochemistry / Year: 2016
Title: The Structure of Carbonic Anhydrase IX Is Adapted for Low-pH Catalysis.
Authors: Mahon, B.P. / Bhatt, A. / Socorro, L. / Driscoll, J.M. / Okoh, C. / Lomelino, C.L. / Mboge, M.Y. / Kurian, J.J. / Tu, C. / Agbandje-McKenna, M. / Frost, S.C. / McKenna, R.
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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_validate_symm_contact / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,08516
Polymers57,0422
Non-polymers1,04314
Water11,277626
1
A: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,18710
Polymers28,5211
Non-polymers6669
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8986
Polymers28,5211
Non-polymers3775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.877, 102.744, 108.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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: 28521.043 Da / Num. of mol.: 2 / Fragment: catalytic-domain (UNP residues 140-399) / Mutation: C161S, L180S, A210K, A258K, F259Y, M360S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA9, G250, MN / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q16790, carbonic anhydrase

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Non-polymers , 5 types, 640 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris HCl, pH 8.5, 8% (w/v) PEG 8000 / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9177 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9177 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 86682 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 12.88 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.04 / Rrim(I) all: 0.108 / Χ2: 0.945 / Net I/av σ(I): 19.738 / Net I/σ(I): 5.9 / Num. measured all: 622633
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.636.70.56542460.8930.2330.6120.72899.3
1.63-1.667.10.50443130.9180.2020.5440.721100
1.66-1.697.10.4642750.9240.1840.4960.735100
1.69-1.727.20.38842810.9380.1550.4180.746100
1.72-1.767.20.3342930.9550.1320.3560.744100
1.76-1.87.20.28642590.9670.1140.3080.754100
1.8-1.857.20.25743340.9720.1020.2770.775100
1.85-1.97.20.22342800.9780.0890.240.77100
1.9-1.957.30.19642970.980.0780.2110.845100
1.95-2.027.30.16243270.9870.0640.1750.821100
2.02-2.097.30.13642900.990.0540.1470.863100
2.09-2.177.30.1243200.9920.0480.1290.84100
2.17-2.277.30.11743100.9920.0460.1260.929100
2.27-2.397.30.10443290.9930.0410.1120.894100
2.39-2.547.30.08943590.9950.0350.0960.908100
2.54-2.737.30.0843440.9950.0320.0870.99100
2.73-3.017.30.07343680.9960.0290.0791.093100
3.01-3.447.20.06744090.9960.0270.0731.278100
3.44-4.337.10.06744300.9950.0270.0721.686100
4.33-206.80.06946180.9940.0280.0741.72799.4

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IAI

3iai


Resolution: 1.598→19.835 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1913 3607 2.32 %Random selection
Rwork0.1678 ---
obs0.1683 77844 93.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.598→19.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3992 0 51 626 4669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074324
X-RAY DIFFRACTIONf_angle_d1.1515897
X-RAY DIFFRACTIONf_dihedral_angle_d15.3371644
X-RAY DIFFRACTIONf_chiral_restr0.047641
X-RAY DIFFRACTIONf_plane_restr0.006777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5976-1.61860.2348850.2073827X-RAY DIFFRACTION61
1.6186-1.64080.2980.19694450X-RAY DIFFRACTION71
1.6408-1.66420.22591140.19524536X-RAY DIFFRACTION73
1.6642-1.68910.2011210.19644902X-RAY DIFFRACTION78
1.6891-1.71540.2171070.19015162X-RAY DIFFRACTION83
1.7154-1.74350.2191340.18765449X-RAY DIFFRACTION87
1.7435-1.77360.23611440.18245691X-RAY DIFFRACTION92
1.7736-1.80580.1881250.1826014X-RAY DIFFRACTION95
1.8058-1.84050.21441520.1816001X-RAY DIFFRACTION97
1.8405-1.87810.22321560.1916168X-RAY DIFFRACTION99
1.8781-1.91890.20031220.19286213X-RAY DIFFRACTION99
1.9189-1.96350.18011580.18896256X-RAY DIFFRACTION100
1.9635-2.01250.21091450.17626290X-RAY DIFFRACTION100
2.0125-2.06690.21831430.17696240X-RAY DIFFRACTION100
2.0669-2.12760.18071520.17526216X-RAY DIFFRACTION100
2.1276-2.19620.23911430.18296253X-RAY DIFFRACTION100
2.1962-2.27460.24841530.17676253X-RAY DIFFRACTION100
2.2746-2.36560.19091440.17216233X-RAY DIFFRACTION100
2.3656-2.4730.21211590.16936266X-RAY DIFFRACTION100
2.473-2.60310.20261480.16456229X-RAY DIFFRACTION100
2.6031-2.76580.17411660.1656262X-RAY DIFFRACTION100
2.7658-2.97870.19871470.16936202X-RAY DIFFRACTION100
2.9787-3.27730.17651550.16316260X-RAY DIFFRACTION100
3.2773-3.74870.18321490.15066239X-RAY DIFFRACTION100
3.7487-4.71250.14441420.13116272X-RAY DIFFRACTION100
4.7125-19.83680.14921450.15726196X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 2.0796 Å / Origin y: 3.4303 Å / Origin z: -6.2038 Å
111213212223313233
T0.0689 Å2-0 Å2-0.0111 Å2-0.0632 Å2-0.0043 Å2--0.0775 Å2
L0.0381 °2-0.012 °20.0289 °2-0.0295 °2-0.2685 °2--0.7488 °2
S0.0026 Å °0.028 Å °0.0043 Å °0.0472 Å °-0.0303 Å °-0.0048 Å °-0.1097 Å °0.0061 Å °-0.035 Å °
Refinement TLS groupSelection details: all

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