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- PDB-6w5e: Class D beta-lactamase BSU-2 -

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Basic information

Entry
Database: PDB / ID: 6w5e
TitleClass D beta-lactamase BSU-2
ComponentsBSU-2 beta-lactamase
KeywordsHYDROLASE / antibiotic resistance / beta-lactamase / Gram-positive / class D
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
MALONATE ION / Probable beta-lactamase YbxI
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSmith, C.A. / Vakulenko, S.B. / Stewart, N.K. / Toth, M.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI114668
CitationJournal: J.Struct.Biol. / Year: 2020
Title: A surface loop modulates activity of the Bacillus class D beta-lactamases.
Authors: Stewart, N.K. / Bhattacharya, M. / Toth, M. / Smith, C.A. / Vakulenko, S.B.
History
DepositionMar 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BSU-2 beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1606
Polymers30,7301
Non-polymers4305
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.625, 47.625, 208.208
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein BSU-2 beta-lactamase / Probable beta-lactamase YbxI


Mass: 30729.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: ybxI, ybdS, BSU02090 / Production host: Escherichia coli (E. coli) / References: UniProt: P54427, beta-lactamase
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 1.92 Å3/Da / Density % sol: 35.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.2 M sodium malonate pH 4.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: May 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.26→46.4 Å / Num. obs: 62108 / % possible obs: 94.7 % / Redundancy: 9.5 % / Biso Wilson estimate: 12.3 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.027 / Rrim(I) all: 0.086 / Net I/σ(I): 13
Reflection shellResolution: 1.26→1.29 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3191 / CC1/2: 0.703 / Rpim(I) all: 0.336 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CTM

5ctm


Resolution: 1.3→43.308 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1721 2824 4.96 %
Rwork0.1521 --
obs0.1532 56927 94.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.68 Å2 / Biso mean: 17.3284 Å2 / Biso min: 8.83 Å2
Refinement stepCycle: final / Resolution: 1.3→43.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 37 211 2192
Biso mean--27.63 28.69 -
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052060
X-RAY DIFFRACTIONf_angle_d0.8292778
X-RAY DIFFRACTIONf_dihedral_angle_d8.0791231
X-RAY DIFFRACTIONf_chiral_restr0.08296
X-RAY DIFFRACTIONf_plane_restr0.005360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3-1.32240.2531320.18712839100
1.3224-1.34650.19991340.17362801100
1.3465-1.37240.22341630.1742788100
1.3724-1.40040.21721470.1572850100
1.4004-1.43080.17761460.1452788100
1.4308-1.46410.20181680.14872794100
1.4641-1.50070.21811530.14022835100
1.5007-1.54130.18931470.13482829100
1.5413-1.58670.20151350.13072857100
1.5867-1.63790.18611330.12892845100
1.6379-1.69640.17361730.1292808100
1.6964-1.76440.23091200.1583241284
1.7644-1.84470.19531530.14422828100
1.8447-1.94190.2565810.1798149452
1.9419-2.06360.16341070.1443228179
2.0636-2.22290.17591430.14372879100
2.2229-2.44660.17811430.15172910100
2.4466-2.80050.16771210.1625238880
2.8005-3.52820.16311630.1559287797
3.5282-43.3080.12921620.1559300094

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