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- PDB-5glc: Crystal structure of the class A beta-lactamase PenL-tTR11 contai... -

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Basic information

Entry
Database: PDB / ID: 5glc
TitleCrystal structure of the class A beta-lactamase PenL-tTR11 containing 20 residues insertion in omega-loop
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta0lactamase / PenL-tTR11 / omega-loop
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / 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
Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsChoi, J.M. / Yi, H. / Kim, H.S. / Lee, S.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation2010-0005114 Korea, Republic Of
National Research Foundation2013R1A1A2057465 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2016
Title: High adaptability of the omega loop underlies the substrate-spectrum-extension evolution of a class A beta-lactamase, PenL
Authors: Yi, H. / Choi, J.M. / Hwang, J. / Prati, F. / Cao, T.P. / Lee, S.H. / Kim, H.S.
History
DepositionJul 10, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)30,7781
Polymers30,7781
Non-polymers00
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11090 Å2
Unit cell
Length a, b, c (Å)69.486, 97.242, 34.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Beta-lactamase


Mass: 30777.803 Da / Num. of mol.: 1 / Fragment: UNP residues 31-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Gene: A8H35_31635 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A2Z4SUB5, UniProt: Q2T5A3*PLUS, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 1.89 Å3/Da / Density % sol: 35.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Tris pH 7.5, 30% PEGMME, 0.1M K-thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2013
RadiationMonochromator: DCM Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 31195 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.2 % / Rmerge(I) obs: 0.074 / Net I/av σ(I): 55.538 / Net I/σ(I): 15.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 12.263 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GL9

5gl9


Resolution: 1.601→32.717 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 17.27
RfactorNum. reflection% reflectionSelection details
Rfree0.1844 1567 5.05 %random
Rwork0.1599 ---
obs0.1611 31041 99.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.601→32.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 0 268 2205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071967
X-RAY DIFFRACTIONf_angle_d1.1242668
X-RAY DIFFRACTIONf_dihedral_angle_d12.302712
X-RAY DIFFRACTIONf_chiral_restr0.074307
X-RAY DIFFRACTIONf_plane_restr0.005353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6009-1.65250.20831200.17352603X-RAY DIFFRACTION98
1.6525-1.71160.21811270.17352661X-RAY DIFFRACTION99
1.7116-1.78010.22791680.17482612X-RAY DIFFRACTION100
1.7801-1.86110.19971390.16212624X-RAY DIFFRACTION99
1.8611-1.95930.19381520.15312639X-RAY DIFFRACTION100
1.9593-2.0820.16691480.15482653X-RAY DIFFRACTION100
2.082-2.24270.1821390.1482695X-RAY DIFFRACTION100
2.2427-2.46830.18191210.16012702X-RAY DIFFRACTION100
2.4683-2.82530.1991550.17092691X-RAY DIFFRACTION100
2.8253-3.55890.18441550.15332710X-RAY DIFFRACTION100
3.5589-32.72430.16061430.15992884X-RAY DIFFRACTION99

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