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- PDB-6w5f: Class D beta-lactamase BSU-2 delta mutant -

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Basic information

Entry
Database: PDB / ID: 6w5f
TitleClass D beta-lactamase BSU-2 delta mutant
Components(BSU-2delta mutant) x 2
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 / beta-lactamase activity / 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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / DI(HYDROXYETHYL)ETHER / Probable beta-lactamase YbxI
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: BSU-2delta mutant
B: BSU-2delta mutant
C: BSU-2delta mutant
D: BSU-2delta mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,11413
Polymers121,3484
Non-polymers7679
Water14,322795
1
A: BSU-2delta mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5273
Polymers30,3581
Non-polymers1682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BSU-2delta mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6264
Polymers30,3151
Non-polymers3103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BSU-2delta mutant


Theoretical massNumber of molelcules
Total (without water)30,3581
Polymers30,3581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: BSU-2delta mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6045
Polymers30,3151
Non-polymers2884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.264, 67.271, 254.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 30358.436 Da / Num. of mol.: 2 / Fragment: side chain of K104 is carboxylated / Mutation: RLT deletion
Source method: isolated from a genetically manipulated source
Details: three residues (RLT) deleted from BSU-2 to produce BSU-2delta
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ybxI, ybdS, BSU02090 / Production host: Escherichia coli (E. coli) / References: UniProt: P54427, beta-lactamase
#2: Protein BSU-2delta mutant / Probable beta-lactamase YbxI


Mass: 30315.436 Da / Num. of mol.: 2 / Fragment: K104 is unmodified / Mutation: RLT deletion
Source method: isolated from a genetically manipulated source
Details: three residues (RLT) deleted from BSU-2 to produce BSU-2delta
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ybxI, ybdS, BSU02090 / Production host: Escherichia coli (E. coli) / References: UniProt: P54427, beta-lactamase

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Non-polymers , 4 types, 804 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 795 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 4% Tacsimate pH 5.0, 12% 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 PILATUS3 6M / Detector: PIXEL / Date: May 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.5→127.3 Å / Num. obs: 181693 / % possible obs: 98.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 17.2 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Net I/σ(I): 14.9
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 8825 / CC1/2: 0.6 / Rpim(I) all: 0.477

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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: 1.5→40.6 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 18.92
RfactorNum. reflection% reflection
Rfree0.191 8974 4.94 %
Rwork0.1526 --
obs0.1546 181558 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.27 Å2 / Biso mean: 24.9427 Å2 / Biso min: 10.05 Å2
Refinement stepCycle: final / Resolution: 1.5→40.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7624 0 63 807 8494
Biso mean--51.8 35.7 -
Num. residues----938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057986
X-RAY DIFFRACTIONf_angle_d0.77810797
X-RAY DIFFRACTIONf_dihedral_angle_d8.526546
X-RAY DIFFRACTIONf_chiral_restr0.051161
X-RAY DIFFRACTIONf_plane_restr0.0051391
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.5170.29322890.2282563597
1.517-1.53490.25052730.2123573098
1.5349-1.55360.25682900.2049563398
1.5536-1.57330.25452930.1972556096
1.5733-1.5940.22573180.1783554996
1.594-1.61580.23962460.1761578898
1.6158-1.63890.21962450.1676572797
1.6389-1.66340.23742800.1793569198
1.6634-1.68940.2432910.1764571698
1.6894-1.71710.23163000.1615569398
1.7171-1.74670.21972610.1508577399
1.7467-1.77840.21773040.1402571698
1.7784-1.81260.17763110.1375574999
1.8126-1.84960.19963400.1339571899
1.8496-1.88990.19242900.1303542994
1.8899-1.93380.17673220.1349577598
1.9338-1.98220.19033160.1439581899
1.9822-2.03580.2132990.1489576199
2.0358-2.09570.19752870.1481573198
2.0957-2.16330.20122320.1443590799
2.1633-2.24060.18963000.1468582399
2.2406-2.33030.18833110.1463577599
2.3303-2.43640.19522730.151552794
2.4364-2.56480.20743020.15535885100
2.5648-2.72550.20133040.1625588199
2.7255-2.93580.20273670.16015834100
2.9358-3.23120.19573590.16325877100
3.2312-3.69840.18462990.1552575596
3.6984-4.65860.15173520.13325977100
4.6586-40.60.16863200.1522615197

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