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- PDB-6d2m: Beta Carbonic anhydrase in complex with thiocyanate -

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Basic information

Entry
Database: PDB / ID: 6d2m
TitleBeta Carbonic anhydrase in complex with thiocyanate
ComponentsCarbonic anhydrase
KeywordsLYASE / Beta CA / carbonic anhydrase / thiocyanate
Function / homology
Function and homology information


carbon utilization / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Prokaryotic-type carbonic anhydrases signature 2. / Carbonic anhydrase, prokaryotic-like, conserved site / Beta-carbonic Anhydrase; Chain A / Carbonic anhydrase / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Carbonic anhydrase / Carbonic anhydrase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsMurray, A. / Aggarwal, M. / Pinard, M. / McKenna, R.
CitationJournal: ChemMedChem / Year: 2018
Title: Structural Mapping of Anion Inhibitors to beta-Carbonic Anhydrase psCA3 from Pseudomonas aeruginosa.
Authors: Murray, A.B. / Aggarwal, M. / Pinard, M. / Vullo, D. / Patrauchan, M. / Supuran, C.T. / McKenna, R.
History
DepositionApr 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8714
Polymers23,6681
Non-polymers2043
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,48616
Polymers94,6724
Non-polymers81412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area16860 Å2
ΔGint-83 kcal/mol
Surface area31380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.614, 77.533, 87.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

21A-427-

HOH

31A-453-

HOH

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Components

#1: Protein Carbonic anhydrase / / Carbonate dehydratase


Mass: 23667.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1G5JF57, UniProt: Q9HVB9*PLUS, 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-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 50% PEG200; 20 mM Tris-HCl; pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→19.8 Å / Num. obs: 18841 / % possible obs: 99.8 % / Redundancy: 3.9 % / Net I/σ(I): 12.9
Reflection shellResolution: 1.9→2 Å

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Processing

Software
NameClassification
HKL-2000data scaling
Cootmodel building
PHENIXrefinement
CrystalCleardata collection
HKL-2000data reduction
RefinementResolution: 1.9→19.8 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.22 --Random selection
Rwork0.18 ---
obs-18841 99.8 %-
Refinement stepCycle: LAST / Resolution: 1.9→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 11 65 1732

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