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- PDB-6y74: X-ray crystal structure of human carbonic anhydrase IX catalytic ... -

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Basic information

Entry
Database: PDB / ID: 6y74
TitleX-ray crystal structure of human carbonic anhydrase IX catalytic domain.
ComponentsCarbonic anhydrase 9
KeywordsLYASE / carbonic anhydrase / proton transfer
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, 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
Similarity search - Domain/homology
ACETATE ION / Carbonic anhydrase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsFisher, S.Z. / Koruza, K.
CitationJournal: Int J Mol Sci / Year: 2020
Title: Biophysical Characterization of Cancer-Related Carbonic Anhydrase IX
Authors: Koruza, K. / Murray, A.B. / Mahon, B.P. / Hopkins, J.B. / Knecht, W. / McKenna, R. / Fisher, S.Z.
History
DepositionFeb 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,89011
Polymers56,5242
Non-polymers1,3669
Water10,395577
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-95 kcal/mol
Surface area22510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.930, 78.340, 74.320
Angle α, β, γ (deg.)90.000, 128.220, 90.000
Int Tables number5
Space group name H-MC121

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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: 28261.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA9, G250, MN / Plasmid: Bac-to-Bac
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q16790, carbonic anhydrase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 584 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.3
Details: 17% PEG 6000, 1.4 M Sodium citrate pH 4.3, 1 M LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.53→37.13 Å / Num. obs: 75610 / % possible obs: 98.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.6
Reflection shellResolution: 1.53→1.56 Å / Rmerge(I) obs: 0.815 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3288

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3iai

3iai


Resolution: 1.53→37.13 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.22
RfactorNum. reflection% reflection
Rfree0.1984 3703 4.9 %
Rwork0.1739 --
obs0.1751 75594 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.55 Å2 / Biso mean: 21.5263 Å2 / Biso min: 7.9 Å2
Refinement stepCycle: final / Resolution: 1.53→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3992 0 80 593 4665
Biso mean--35.51 29.26 -
Num. residues----516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.53-1.550.29671040.27022374247884
1.55-1.570.26551160.25732691280794
1.57-1.60.28041350.22622711284698
1.6-1.620.27171040.21592797290198
1.62-1.650.24021440.21482783292798
1.65-1.670.26661360.20092699283598
1.67-1.70.24261540.18842763291798
1.7-1.730.23331630.18382757292099
1.73-1.770.2131470.18562722286999
1.77-1.80.23411230.18272801292499
1.8-1.840.20941280.1842779290799
1.84-1.880.20661210.19082790291199
1.88-1.930.2261530.18782785293899
1.93-1.980.22211290.16612794292399
1.98-2.040.17961560.16552780293699
2.04-2.110.20941630.1652755291899
2.11-2.180.17151570.16412764292199
2.18-2.270.19681620.167627772939100
2.27-2.370.20021440.17282830297499
2.37-2.50.21421400.176327812921100
2.5-2.660.19071500.177428362986100
2.66-2.860.19661820.180327622944100
2.86-3.150.19371550.174527902945100
3.15-3.60.19131440.157628432987100
3.6-4.540.1551580.143528312989100
4.54-37.130.1881350.171628963031100

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