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- PDB-6yl7: Crystal structure of beta carbonic anhydrase from the pathogenic ... -

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Basic information

Entry
Database: PDB / ID: 6yl7
TitleCrystal structure of beta carbonic anhydrase from the pathogenic bacterium Burkholderia pseudomallei
ComponentsBeta carbonic anhydrase
KeywordsLYASE / carbonic anhydrase / beta carbonic anhydrase / Burkholderia pseudomallei
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. / 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
Carbonic anhydrase 2
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsAngeli, A. / Ferraroni, M.
CitationJournal: Molecules / Year: 2020
Title: Crystal Structure of a Tetrameric Type II beta-Carbonic Anhydrase from the Pathogenic BacteriumBurkholderia pseudomallei.
Authors: Angeli, A. / Ferraroni, M. / Pinteala, M. / Maier, S.S. / Simionescu, B.C. / Carta, F. / Del Prete, S. / Capasso, C. / Supuran, C.T.
History
DepositionApr 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3342
Polymers28,2691
Non-polymers651
Water37821
1
A: Beta carbonic anhydrase
hetero molecules

A: Beta carbonic anhydrase
hetero molecules

A: Beta carbonic anhydrase
hetero molecules

A: Beta carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,3388
Polymers113,0764
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_564x,x-y+1,-z-1/31
Buried area14200 Å2
ΔGint-82 kcal/mol
Surface area30110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.738, 88.738, 112.428
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

21A-410-

HOH

31A-413-

HOH

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Components

#1: Protein Beta carbonic anhydrase / Carbonate dehydratase / Carbonic anhydrase


Mass: 28269.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria)
Gene: can_1, can_2, BOC42_16450, CXQ84_19645, DF122_01465, ERS013345_01543, SAMEA1968934_03740
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A069AXA0, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22% PEG 4000, 10% isopropanol, 100 mM HEPES pH 7.5 and 3% v/v 1,5-Diaminopentene di-HCl.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0399 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0399 Å / Relative weight: 1
ReflectionResolution: 3.17→45.41 Å / Num. obs: 4883 / % possible obs: 99.9 % / Redundancy: 24.7 % / CC1/2: 1 / Rmerge(I) obs: 0.341 / Rpim(I) all: 0.093 / Rrim(I) all: 0.354 / Net I/σ(I): 9.7
Reflection shellResolution: 3.17→3.38 Å / Rmerge(I) obs: 2.96 / Num. unique obs: 849 / CC1/2: 1 / Rpim(I) all: 0.84 / Rrim(I) all: 3.08

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4rxy

4rxy


Resolution: 3.17→45.41 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.927 / SU B: 33.699 / SU ML: 0.536 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.557
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2962 208 4.3 %RANDOM
Rwork0.1926 ---
obs0.197 4605 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 199.45 Å2 / Biso mean: 90.296 Å2 / Biso min: 45.04 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å21 Å20 Å2
2--2.01 Å2-0 Å2
3----6.51 Å2
Refinement stepCycle: final / Resolution: 3.17→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1548 0 1 21 1570
Biso mean--100.46 75.26 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131583
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171374
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.6192171
X-RAY DIFFRACTIONr_angle_other_deg1.2761.573140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9465209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.68422.37580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.12815205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.564159
X-RAY DIFFRACTIONr_chiral_restr0.0590.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021853
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02334
LS refinement shellResolution: 3.17→3.248 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.493 15 -
Rwork0.39 305 -
obs--93.29 %

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