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

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Basic information

Entry
Database: PDB / ID: 6yjn
TitleCrystal structure of beta carbonic anhydrase from the pathogenic bacterium Burkholderia pseudomallei.
ComponentsBeta carbonic anhydrase
KeywordsLYASE / 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 / Carbonic anhydrase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 3, 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
Water93752
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 area13140 Å2
ΔGint-83 kcal/mol
Surface area31310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.031, 88.031, 111.644
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-420-

HOH

21A-432-

HOH

31A-435-

HOH

41A-439-

HOH

51A-451-

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, UniProt: Q63Y17*PLUS, 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 / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 22% PEG 4000, 10% isopropanol, 100 mM HEPES pH 8.5 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: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→45.49 Å / Num. obs: 7508 / % possible obs: 99.9 % / Redundancy: 32.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.067 / Rrim(I) all: 0.288 / Net I/σ(I): 12.6
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 8.711 / Num. unique obs: 968 / CC1/2: 0.415 / Rpim(I) all: 2.059 / Rrim(I) all: 8.953

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless5.8.0258data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4rxy

4rxy


Resolution: 2.7→45.08 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.894 / SU B: 22.437 / SU ML: 0.424 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.859 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3223 387 5.2 %RANDOM
Rwork0.2133 ---
obs0.2192 7093 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 202.03 Å2 / Biso mean: 81.594 Å2 / Biso min: 49.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.05 Å2-0 Å2
2---0.11 Å2-0 Å2
3---0.35 Å2
Refinement stepCycle: final / Resolution: 2.7→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 0 1 52 1588
Biso mean--89.69 84.1 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0121569
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.6132154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8745211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27322.91772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.72515197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.601157
X-RAY DIFFRACTIONr_chiral_restr0.1160.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021221
LS refinement shellResolution: 2.701→2.771 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 29 -
Rwork0.415 507 -
all-536 -
obs--100 %

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