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- PDB-5gs8: Crystal structure of TLA-3 extended-spectrum beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 5gs8
TitleCrystal structure of TLA-3 extended-spectrum beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / extended-spectrum beta-lactamase
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 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
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsWachino, J. / Jin, W. / Arakawa, Y.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2017
Title: Structural Insights into the TLA-3 Extended-Spectrum beta-Lactamase and Its Inhibition by Avibactam and OP0595.
Authors: Jin, W. / Wachino, J. / Yamaguchi, Y. / Kimura, K. / Kumar, A. / Yamada, M. / Morinaka, A. / Sakamaki, Y. / Yonezawa, M. / Kurosaki, H. / Arakawa, Y.
History
DepositionAug 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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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)32,24323
Polymers31,3471
Non-polymers89622
Water5,945330
1
A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,48646
Polymers62,6942
Non-polymers1,79244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9140 Å2
ΔGint-493 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.850, 67.930, 45.060
Angle α, β, γ (deg.)90.00, 94.17, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-534-

HOH

21A-638-

HOH

31A-663-

HOH

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Components

#1: Protein Beta-lactamase / Extended-spectrum beta-lactamase TLA-3


Mass: 31346.771 Da / Num. of mol.: 1 / Fragment: UNP residues 30-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B6VPP7, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium citrate, 2.8M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.59→55.18 Å / Num. obs: 38203 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 24.7
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 9.4 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+25 / Resolution: 1.59→55.18 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.105 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.07 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16046 1903 5 %RANDOM
Rwork0.13517 ---
obs0.13643 36315 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.726 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å2-0.54 Å2
2--0.49 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.59→55.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 42 330 2543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192320
X-RAY DIFFRACTIONr_bond_other_d0.0010.022266
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.973154
X-RAY DIFFRACTIONr_angle_other_deg0.77135277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4365302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94126.39297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74115454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.217152
X-RAY DIFFRACTIONr_chiral_restr0.1030.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022576
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02486
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5531.1541127
X-RAY DIFFRACTIONr_mcbond_other1.5431.1511126
X-RAY DIFFRACTIONr_mcangle_it2.1781.7261414
X-RAY DIFFRACTIONr_mcangle_other2.1781.7291415
X-RAY DIFFRACTIONr_scbond_it3.0721.4711193
X-RAY DIFFRACTIONr_scbond_other2.9731.4541174
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.362.0371697
X-RAY DIFFRACTIONr_long_range_B_refined5.83517.5723106
X-RAY DIFFRACTIONr_long_range_B_other5.66316.2412927
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.591→1.632 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 143 -
Rwork0.173 2664 -
obs--99.61 %

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