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- PDB-6w34: Crystal Structure of Class A Beta-lactamase from Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 6w34
TitleCrystal Structure of Class A Beta-lactamase from Bacillus cereus
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamases / Antibiotic Resistant / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of Class A Beta-lactamase from Bacillus cereus
Authors: Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1409
Polymers68,6642
Non-polymers4767
Water5,567309
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6506
Polymers34,3321
Non-polymers3185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4903
Polymers34,3321
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.809, 43.835, 68.612
Angle α, β, γ (deg.)94.945, 91.382, 92.794
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Beta-lactamase


Mass: 34332.105 Da / Num. of mol.: 2 / Mutation: A278T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: BC_2473 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q81DA0, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.87 Å3/Da / Density % sol: 34.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M Magnesium chloride, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 78371 / % possible obs: 89.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.42 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.098 / Net I/σ(I): 17.1
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 3428 / CC1/2: 0.622 / % possible all: 78.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 3QHY

3qhy


Resolution: 1.45→43.61 Å / SU ML: 0.1556 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.492
RfactorNum. reflection% reflection
Rfree0.197 3666 4.69 %
Rwork0.1591 --
obs0.1609 78242 89.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.95 Å2
Refinement stepCycle: LAST / Resolution: 1.45→43.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3987 0 27 309 4323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00484174
X-RAY DIFFRACTIONf_angle_d0.74985662
X-RAY DIFFRACTIONf_chiral_restr0.0746646
X-RAY DIFFRACTIONf_plane_restr0.0043739
X-RAY DIFFRACTIONf_dihedral_angle_d20.12671546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.3438860.28382163X-RAY DIFFRACTION66.46
1.47-1.490.29081650.23892797X-RAY DIFFRACTION87.3
1.49-1.510.22161290.20642849X-RAY DIFFRACTION88.34
1.51-1.530.25081440.19832901X-RAY DIFFRACTION89.11
1.53-1.560.24421400.18252850X-RAY DIFFRACTION89.95
1.56-1.580.24121300.17122896X-RAY DIFFRACTION88.77
1.58-1.610.21651470.16262841X-RAY DIFFRACTION88.9
1.61-1.640.21111290.14922816X-RAY DIFFRACTION86.72
1.64-1.670.21070.14532663X-RAY DIFFRACTION81.98
1.67-1.710.22381420.13932930X-RAY DIFFRACTION90.65
1.71-1.740.19061560.13762987X-RAY DIFFRACTION92.71
1.74-1.780.20541530.13162960X-RAY DIFFRACTION91.99
1.78-1.830.17661450.13122905X-RAY DIFFRACTION91.18
1.83-1.880.19151630.13422886X-RAY DIFFRACTION90.66
1.88-1.930.20141330.13092858X-RAY DIFFRACTION88.31
1.93-1.990.17441760.1342651X-RAY DIFFRACTION83.54
1.99-2.070.16941650.1352990X-RAY DIFFRACTION92.93
2.07-2.150.20211260.13913003X-RAY DIFFRACTION92.96
2.15-2.250.20191270.13932989X-RAY DIFFRACTION92.96
2.25-2.370.19391450.14982997X-RAY DIFFRACTION91.95
2.37-2.510.18781600.15032853X-RAY DIFFRACTION89.09
2.51-2.710.21251430.17042888X-RAY DIFFRACTION89.83
2.71-2.980.20121320.1823066X-RAY DIFFRACTION94.59
2.98-3.410.23721260.17732994X-RAY DIFFRACTION92.55
3.41-4.30.18951140.16062905X-RAY DIFFRACTION88.98
4.3-43.610.17671830.15842938X-RAY DIFFRACTION92.69

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