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- PDB-5hw3: Crystal structure of a beta lactamase from Burkholderia vietnamiensis -

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Basic information

Entry
Database: PDB / ID: 5hw3
TitleCrystal structure of a beta lactamase from Burkholderia vietnamiensis
ComponentsBeta-lactamase
KeywordsHYDROLASE / SSGCID / beta lactamase / Burkholderia vietnamiensis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 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
ACETATE ION / Beta-lactamase
Similarity search - Component
Biological speciesBurkholderia vietnamiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a beta lactamase from Burkholderia vietnamiensis
Authors: Potts, K.T. / Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJan 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,85512
Polymers28,9101
Non-polymers94611
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.430, 69.420, 78.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase /


Mass: 28909.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia vietnamiensis (bacteria) / Strain: G4 / LMG 22486 / Gene: Bcep1808_4738 / Plasmid: BuviA.00104.a.B2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4JN42, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 1.86 Å3/Da / Density % sol: 32 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: JCSG+ A1: 50% (v/v) PEG 400, 200mM Lithium Sulfate, 100mM Sodium Acetate/Acetic acid pH 4.5; 3mM MgCl2, 3mM UTP; BuviA.00104.a.B2 at 20mg/Ml; direct cryo; tray 267206a1; puck wmo4-4 aps21idf

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 11, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 40687 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 8.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.071 / Χ2: 0.979 / Net I/av σ(I): 20.87 / Net I/σ(I): 20.87 / Num. measured all: 284886
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.45-1.4950.3743.9713558298727190.9090.41891
1.49-1.530.325.3116915290528470.9450.3598
1.53-1.570.2756.9920417283228320.9660.296100
1.57-1.620.2418.0420031276027600.9760.259100
1.62-1.670.2059.419437267126710.980.221100
1.67-1.730.17710.9618991260726060.9860.19100
1.73-1.80.1413.3818276250625060.9910.15100
1.8-1.870.11316.6117580240724060.9930.121100
1.87-1.960.09219.5316711228722840.9960.09999.9
1.96-2.050.07423.516294223122320.9970.08100
2.05-2.160.06327.2115526212221200.9980.06799.9
2.16-2.290.05530.6714772201520130.9980.05999.9
2.29-2.450.05132.8513907190519040.9980.05499.9
2.45-2.650.04735.4312667174017380.9980.05199.9
2.65-2.90.04438.1312047165916580.9980.04799.9
2.9-3.240.03942.1910651147714770.9980.042100
3.24-3.740.03547.469566134213420.9990.038100
3.74-4.590.03249.517959112811260.9990.03599.8
4.59-6.480.03147.8961868998990.9990.034100
6.48-500.0346.5933955565470.9990.03298.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXdev_2264refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C6Y

4c6y


Resolution: 1.45→34.21 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1621 2031 5 %random selection
Rwork0.129 38595 --
obs0.1307 40626 99.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.43 Å2 / Biso mean: 11.7865 Å2 / Biso min: 4 Å2
Refinement stepCycle: final / Resolution: 1.45→34.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 52 280 2351
Biso mean--29.44 23.78 -
Num. residues----269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072202
X-RAY DIFFRACTIONf_angle_d1.0543011
X-RAY DIFFRACTIONf_chiral_restr0.084333
X-RAY DIFFRACTIONf_plane_restr0.007402
X-RAY DIFFRACTIONf_dihedral_angle_d18.728828
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.48380.21231260.1472334246091
1.4838-1.52090.18591310.13192472260397
1.5209-1.5620.19461360.121525392675100
1.562-1.6080.16971360.113125652701100
1.608-1.65990.17281160.112225912707100
1.6599-1.71920.16061220.110225652687100
1.7192-1.7880.14241400.111525652705100
1.788-1.86940.16551440.113625672711100
1.8694-1.96790.15691340.11425882722100
1.9679-2.09120.1591420.108725562698100
2.0912-2.25260.13691300.113726102740100
2.2526-2.47930.15381460.125525832729100
2.4793-2.83790.14881310.141726352766100
2.8379-3.57480.16131610.142726292790100
3.5748-34.21930.17481360.153227962932100

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