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- PDB-5cxk: Crystal structure of beta carbonic anhydrase from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 5cxk
TitleCrystal structure of beta carbonic anhydrase from Vibrio cholerae
ComponentsCarbonic anhydrase
KeywordsLYASE
Function / homology
Function and homology information


carbon utilization / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Prokaryotic-type carbonic anhydrases signature 1. / 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
BICARBONATE ION / Carbonic anhydrase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsFerraroni, M. / Supuran, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Crystal structure and kinetic studies of a tetrameric type II beta-carbonic anhydrase from the pathogenic bacterium Vibrio cholerae.
Authors: Ferraroni, M. / Del Prete, S. / Vullo, D. / Capasso, C. / Supuran, C.T.
History
DepositionJul 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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
B: Carbonic anhydrase
H: Carbonic anhydrase
G: Carbonic anhydrase
D: Carbonic anhydrase
C: Carbonic anhydrase
F: Carbonic anhydrase
E: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,47822
Polymers201,5898
Non-polymers88914
Water15,043835
1
A: Carbonic anhydrase
B: Carbonic anhydrase
D: Carbonic anhydrase
C: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,30012
Polymers100,7944
Non-polymers5068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16810 Å2
ΔGint-90 kcal/mol
Surface area31480 Å2
MethodPISA
2
H: Carbonic anhydrase
G: Carbonic anhydrase
F: Carbonic anhydrase
E: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,17810
Polymers100,7944
Non-polymers3846
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16490 Å2
ΔGint-95 kcal/mol
Surface area31340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.087, 84.087, 316.378
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Carbonic anhydrase


Mass: 25198.596 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: can, DN30_1616 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A086SLX8, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CHO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 835 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG8000, ethylene glycol,Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→47.5 Å / Num. obs: 166608 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 28.602 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.092 / Χ2: 0.954 / Net I/σ(I): 10.82 / Num. measured all: 501239
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-2.0120.6510.4331.624551114309131590.58787.1
2.02-2.160.8860.3354.477490413526134890.36999.7
2.16-2.330.9570.2117.677655112591125380.23199.6
2.33-2.550.9780.15610.767290911635115620.1799.4
2.55-2.850.9920.10615.976695910570104630.11599
2.85-3.290.9960.07323.0158665940892600.07998.4
3.29-4.030.9970.05132.2148155805978830.05697.8
4.03-5.670.9980.04436.3435980636761490.04896.6
5.670.9990.03634.7321605382235910.0494

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.527
Highest resolutionLowest resolution
Rotation47.51 Å3 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ESF

2esf


Resolution: 1.9→47.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.904 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.1818 / FOM work R set: 0.8466 / SU B: 2.157 / SU ML: 0.07 / SU R Cruickshank DPI: 0.0295 / SU Rfree: 0.0302 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 8261 5 %RANDOM
Rwork0.1831 ---
obs0.1858 158223 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.55 Å2 / Biso mean: 22.753 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å2-0 Å2-0 Å2
2---0.81 Å2-0 Å2
3---1.63 Å2
Refinement stepCycle: final / Resolution: 1.9→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14076 0 32 835 14943
Biso mean--22.87 22.49 -
Num. residues----1776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01914418
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9419586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38851772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83824.403729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.474152367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5731588
X-RAY DIFFRACTIONr_chiral_restr0.0880.22147
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111140
X-RAY DIFFRACTIONr_mcbond_it0.9272.2727100
X-RAY DIFFRACTIONr_mcangle_it1.4593.4058862
X-RAY DIFFRACTIONr_scbond_it0.8692.3097318
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 584 -
Rwork0.207 9890 -
all-10474 -
obs--82.61 %

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