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- PDB-6w5o: Class D beta-lactamase BAT-2 delta mutant -

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Basic information

Entry
Database: PDB / ID: 6w5o
TitleClass D beta-lactamase BAT-2 delta mutant
ComponentsBAT-2 Beta-lactamase delta mutant
KeywordsHYDROLASE / antibiotic resistance / beta-lactamase / Gram-positive / class D
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
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
CITRATE ANION / Beta-lactamase
Similarity search - Component
Biological speciesBacillus atrophaeus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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

Downloads & links

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Assembly

Deposited unit
A: BAT-2 Beta-lactamase delta mutant
B: BAT-2 Beta-lactamase delta mutant
C: BAT-2 Beta-lactamase delta mutant
D: BAT-2 Beta-lactamase delta mutant
E: BAT-2 Beta-lactamase delta mutant
F: BAT-2 Beta-lactamase delta mutant
G: BAT-2 Beta-lactamase delta mutant
H: BAT-2 Beta-lactamase delta mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,86410
Polymers245,6138
Non-polymers2512
Water3,243180
1
A: BAT-2 Beta-lactamase delta mutant


Theoretical massNumber of molelcules
Total (without water)30,7021
Polymers30,7021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BAT-2 Beta-lactamase delta mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8912
Polymers30,7021
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BAT-2 Beta-lactamase delta mutant


Theoretical massNumber of molelcules
Total (without water)30,7021
Polymers30,7021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: BAT-2 Beta-lactamase delta mutant


Theoretical massNumber of molelcules
Total (without water)30,7021
Polymers30,7021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: BAT-2 Beta-lactamase delta mutant


Theoretical massNumber of molelcules
Total (without water)30,7021
Polymers30,7021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: BAT-2 Beta-lactamase delta mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7642
Polymers30,7021
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: BAT-2 Beta-lactamase delta mutant


Theoretical massNumber of molelcules
Total (without water)30,7021
Polymers30,7021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: BAT-2 Beta-lactamase delta mutant


Theoretical massNumber of molelcules
Total (without water)30,7021
Polymers30,7021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.433, 66.178, 134.009
Angle α, β, γ (deg.)90.000, 91.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BAT-2 Beta-lactamase delta mutant


Mass: 30701.635 Da / Num. of mol.: 8 / Mutation: RLT deletion
Source method: isolated from a genetically manipulated source
Details: three residue (RLT) deletion in each monomer / Source: (gene. exp.) Bacillus atrophaeus (bacteria) / Strain: 1942 / Gene: BATR1942_19650 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3EA14, beta-lactamase
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M ammonium citrate pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.55→133.95 Å / Num. obs: 75105 / % possible obs: 98.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 21.4 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.084 / Rrim(I) all: 0.155 / Net I/σ(I): 7.3
Reflection shellResolution: 2.55→2.6 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4334 / CC1/2: 0.684 / Rpim(I) all: 0.424 / Rrim(I) all: 0.774

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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: 2.55→60.561 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 30.63
RfactorNum. reflection% reflection
Rfree0.2905 3572 4.76 %
Rwork0.2169 --
obs0.2204 75011 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.41 Å2 / Biso mean: 32.1091 Å2 / Biso min: 7.67 Å2
Refinement stepCycle: final / Resolution: 2.55→60.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15459 0 23 180 15662
Biso mean--44.81 24.88 -
Num. residues----1872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515896
X-RAY DIFFRACTIONf_angle_d0.68621475
X-RAY DIFFRACTIONf_dihedral_angle_d8.78212176
X-RAY DIFFRACTIONf_chiral_restr0.0462256
X-RAY DIFFRACTIONf_plane_restr0.0042766
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.55-2.58360.38151200.292263895
2.5836-2.6190.34791570.2798275699
2.619-2.65640.38031390.2696277799
2.6564-2.6960.34421320.2707272999
2.696-2.73820.34611470.2667275298
2.7382-2.78310.3341500.2702274999
2.7831-2.8310.39031360.2683273899
2.831-2.88250.35571370.266275298
2.8825-2.9380.3341890.2431267998
2.938-2.99790.30751750.2404271698
2.9979-3.06310.36641300.2444269197
3.0631-3.13440.2831240.2354267194
3.1344-3.21280.32261130.2472271697
3.2128-3.29960.32191600.2485279798
3.2996-3.39670.3578900.2247278599
3.3967-3.50630.30381120.2156278998
3.5063-3.63160.30031380.2072280599
3.6316-3.7770.29651440.2066270898
3.777-3.94890.30131400.1968275397
3.9489-4.1570.22661490.1876267094
4.157-4.41740.25521310.1772277499
4.4174-4.75840.23691350.1717279198
4.7584-5.2370.22031120.1717280999
5.237-5.99420.22591550.1874275996
5.9942-7.54980.2441350.2112279598
7.5498-60.5610.23061220.1944284095

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