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- PDB-5ihv: Crystal structure of a beta-lactamase from Burkholderia ambifaria -

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Basic information

Entry
Database: PDB / ID: 5ihv
TitleCrystal structure of a beta-lactamase from Burkholderia ambifaria
ComponentsBeta-lactamase
KeywordsHYDROLASE / SSGCID / beta-lactamase / Burkholderia ambifaria / 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, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a beta-lactamase from Burkholderia ambifaria
Authors: Mayclin, S.J. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionFeb 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 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_prerelease_seq / 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3153
Polymers28,1911
Non-polymers1242
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.260, 63.080, 73.850
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: 28190.980 Da / Num. of mol.: 1 / Fragment: UNP residues 39-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (bacteria) / Strain: MC40-6 / Gene: BamMC406_4487 / Plasmid: BuamA.00104.a.B2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1YX81, beta-lactamase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.04 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: JCSG+ A7 (267021a7): 100mM CHES pH 9.5, 20% PEG8000, protein conc. 48.83mg/mL; cryo 20% EG; puck uqf3-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 92835 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 9.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 18
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.1-1.130.4962.18189.4
1.13-1.160.4073.17196.7
1.16-1.190.3494.61199.6
1.19-1.230.2915.751100
1.23-1.270.2426.921100
1.27-1.310.2038.261100
1.31-1.360.1719.751100
1.36-1.420.13911.751100
1.42-1.480.10914.72199.9
1.48-1.560.0917.81100
1.56-1.640.07221.391100
1.64-1.740.0625.191100
1.74-1.860.0529.691100
1.86-2.010.04335.091100
2.01-2.20.03839.611100
2.2-2.460.03542.511100
2.46-2.840.03244.991100
2.84-3.480.02947.9199.8
3.48-4.920.02848.84198.8
4.920.02746.18193.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev_2328refinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3w4q

3w4q


Resolution: 1.1→50 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.44
RfactorNum. reflection% reflection
Rfree0.1668 2015 2.17 %
Rwork0.1365 --
obs0.1372 92833 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 46.34 Å2 / Biso mean: 15.5674 Å2 / Biso min: 5.58 Å2
Refinement stepCycle: final / Resolution: 1.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 8 384 2281
Biso mean--21.27 26.66 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122038
X-RAY DIFFRACTIONf_angle_d1.2852804
X-RAY DIFFRACTIONf_chiral_restr0.097335
X-RAY DIFFRACTIONf_plane_restr0.01371
X-RAY DIFFRACTIONf_dihedral_angle_d19.356761
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.12750.20881140.20615816593089
1.1275-1.1580.16681370.16456226636396
1.158-1.1920.16251440.136264656609100
1.192-1.23050.16181710.125164906661100
1.2305-1.27450.16491410.119164776618100
1.2745-1.32550.13991570.112265106667100
1.3255-1.38590.14661530.104565016654100
1.3859-1.45890.13811490.096565296678100
1.4589-1.55030.11661270.094765336660100
1.5503-1.670.16151500.101765846734100
1.67-1.83810.13821200.116765886708100
1.8381-2.1040.15221560.126766206776100
2.104-2.65060.21621570.146266536810100
2.6506-31.88010.17611390.16736826696599

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