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- PDB-6rqw: X-ray crystal structure of perdeuterated (D) small monoclinic uni... -

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Basic information

Entry
Database: PDB / ID: 6rqw
TitleX-ray crystal structure of perdeuterated (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
FORMIC ACID / Carbonic anhydrase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.488 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 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 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 1.3Oct 23, 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)28,2043
Polymers28,0931
Non-polymers1112
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-41 kcal/mol
Surface area11970 Å2
Unit cell
Length a, b, c (Å)44.390, 65.090, 46.600
Angle α, β, γ (deg.)90.000, 114.710, 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 / Mutation: C174S L183S A213K A258K F259Y M350S
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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% (w/v) PEG 4000, 0.2 M ammonium formate, 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: 1.488→40.326 Å / Num. obs: 39461 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.3
Reflection shellResolution: 1.49→1.51 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1948 / % possible all: 99.3

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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: 1.488→40.326 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.82
RfactorNum. reflection% reflection
Rfree0.2033 1869 4.74 %
Rwork0.1725 --
obs0.174 39435 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.18 Å2 / Biso mean: 30.2325 Å2 / Biso min: 13.89 Å2
Refinement stepCycle: final / Resolution: 1.488→40.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 4 212 2202
Biso mean--34.34 37.93 -
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152154
X-RAY DIFFRACTIONf_angle_d1.3442954
X-RAY DIFFRACTIONf_chiral_restr0.1322
X-RAY DIFFRACTIONf_plane_restr0.011392
X-RAY DIFFRACTIONf_dihedral_angle_d25.156824
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4883-1.52860.36861550.357928673022100
1.5286-1.57350.30751590.300628563015100
1.5735-1.62430.29491380.261628562994100
1.6243-1.68240.27511550.218328583013100
1.6824-1.74970.22741470.185828863033100
1.7497-1.82940.21861570.185328763033100
1.8294-1.92580.23811320.181628913023100
1.9258-2.04650.18321330.169829203053100
2.0465-2.20450.21311470.171828793026100
2.2045-2.42630.21021060.176429393045100
2.4263-2.77730.21021430.179428993042100
2.7773-3.49880.17521420.169729143056100
3.4988-40.34120.1871550.14372925308099

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