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- PDB-6rqu: X-ray crystal structure of H/D exchanged (H/D) small monoclinic u... -

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Basic information

Entry
Database: PDB / ID: 6rqu
TitleX-ray crystal structure of H/D exchanged (H/D) small monoclinic unit cell CA IX SV.
ComponentsCarbonic anhydrase 9
KeywordsPROTON TRANSPORT / carbonic anhydrase / CA IX / surface variant
Function / homology
Function and homology information


Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / 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 / microvillus membrane / response to testosterone / 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, 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: 1.393 Å
AuthorsFisher, Z. / Koruza, K.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structural comparison of protiated, H/D-exchanged and deuterated human carbonic anhydrase IX.
Authors: Koruza, K. / Lafumat, B. / Nyblom, M. / Mahon, B.P. / Knecht, W. / McKenna, R. / Fisher, S.Z.
History
DepositionMay 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: 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
Revision 1.2Oct 9, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2173
Polymers28,0931
Non-polymers1242
Water4,576254
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-40 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.450, 65.380, 46.760
Angle α, β, γ (deg.)90.000, 115.120, 90.000
Int Tables number4
Space group name H-MP1211

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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: 28092.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA9, G250, MN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q16790, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% (w/v) PEG 4000, 0.2 M sodium acetate, 0.1 M Tris-HCl pH 8.5

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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 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.39→40 Å / Num. obs: 48352 / % possible obs: 99.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 19.9
Reflection shellResolution: 1.39→1.42 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2406 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dvx

5dvx


Resolution: 1.393→32.69 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.91
RfactorNum. reflection% reflection
Rfree0.1881 2431 5.03 %
Rwork0.1726 --
obs0.1734 48338 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.4 Å2 / Biso mean: 29.7701 Å2 / Biso min: 15.12 Å2
Refinement stepCycle: final / Resolution: 1.393→32.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1978 0 5 255 2238
Biso mean--32.78 37.79 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062205
X-RAY DIFFRACTIONf_angle_d0.9613031
X-RAY DIFFRACTIONf_chiral_restr0.08328
X-RAY DIFFRACTIONf_plane_restr0.007409
X-RAY DIFFRACTIONf_dihedral_angle_d26.046840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3927-1.42120.2581130.264327092822100
1.4212-1.45210.25661280.25427012829100
1.4521-1.48590.27581380.240427242862100
1.4859-1.5230.25191480.213926412789100
1.523-1.56420.23471430.209326882831100
1.5642-1.61020.22981420.196927072849100
1.6102-1.66220.23451560.190226822838100
1.6622-1.72160.21891430.184426932836100
1.7216-1.79050.21561640.189226832847100
1.7905-1.8720.20491580.193527052863100
1.872-1.97070.24571450.195926842829100
1.9707-2.09410.20381290.175227002829100
2.0941-2.25580.20891260.180327392865100
2.2558-2.48270.17131570.181926962853100
2.4827-2.84180.18811450.180727082853100
2.8418-3.57970.16491290.164627462875100
3.5797-32.6990.16691670.14282701286898

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