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- PDB-6mu9: Beta-lactamase penicillinase from Bacillus megaterium -

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Basic information

Entry
Database: PDB / ID: 6mu9
TitleBeta-lactamase penicillinase from Bacillus megaterium
ComponentsBeta-lactamase
KeywordsLIGASE / beta-lactamase / penicillinase / structural genomics / IDP97228 / 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 megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsOsipiuk, J. / Tesar, C. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: to be published
Title: Beta-lactamase penicillinase from Bacillus megaterium
Authors: Osipiuk, J. / Tesar, C. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8022
Polymers30,7061
Non-polymers961
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.307, 42.094, 48.542
Angle α, β, γ (deg.)97.730, 105.520, 113.340
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Beta-lactamase


Mass: 30706.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: DSM 319 / Gene: penP, BMD_3363 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D5DH82, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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 Å3/Da / Density % sol: 38.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris:HCl buffer, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 14, 2018
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 0.97→45.01 Å / Num. obs: 108453 / % possible obs: 76.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.022 / Rrim(I) all: 0.043 / Χ2: 0.92 / Net I/av σ(I): 32.6 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
0.97-0.993.40.2229.117000.9310.140.2632.57124.1
0.99-13.60.17523480.9570.1060.2052.08433.1
1-1.023.70.12831460.9740.0760.1491.36844.8
1.02-1.043.70.09843300.9870.0580.1141.00361.2
1.04-1.073.80.08558190.990.050.0981.03183
1.07-1.093.70.07958990.990.0470.0921.05983.7
1.09-1.123.80.07557890.9920.0440.0871.07982.3
1.12-1.153.80.0755390.9930.0410.0811.05378.7
1.15-1.183.80.06461280.9930.0370.0740.96486.3
1.18-1.223.80.05860720.9940.0340.0680.88286.1
1.22-1.273.80.05358980.9950.0310.0620.85183.6
1.27-1.323.80.0557120.9960.030.0580.77881.3
1.32-1.383.80.04862080.9960.0280.0550.75188.3
1.38-1.453.80.04462210.9970.0260.0510.72688.1
1.45-1.543.80.0460360.9970.0240.0470.69885.4
1.54-1.663.80.03861030.9970.0220.0440.72486.8
1.66-1.833.80.03764370.9970.0220.0430.7591.5
1.83-2.093.80.03362420.9980.020.0380.78488.3
2.09-2.633.80.02963650.9980.0170.0330.72990.6
2.63-503.80.03364610.9970.020.0380.84591.6

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X71

2x71


Resolution: 0.97→45.01 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.311 / SU ML: 0.008 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.019
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1112 5408 5 %RANDOM
Rwork0.1011 ---
obs0.1017 103044 76.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 54.97 Å2 / Biso mean: 8.118 Å2 / Biso min: 2.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0.08 Å2-0.29 Å2
2---0.01 Å2-0.1 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 0.97→45.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 5 430 2491
Biso mean--6.6 18.94 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022267
X-RAY DIFFRACTIONr_bond_other_d0.0010.022199
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9793114
X-RAY DIFFRACTIONr_angle_other_deg0.81535105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8215310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.03625114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2115417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1191517
X-RAY DIFFRACTIONr_chiral_restr0.0940.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212627
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02496
X-RAY DIFFRACTIONr_rigid_bond_restr1.86734466
X-RAY DIFFRACTIONr_sphericity_free26.149556
X-RAY DIFFRACTIONr_sphericity_bonded6.73754778
LS refinement shellResolution: 0.97→0.995 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 155 -
Rwork0.29 2566 -
all-2721 -
obs--26.09 %

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