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- PDB-5x5g: Crystal structure of TLA-3 extended-spectrum beta-lactamase in a ... -

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Basic information

Entry
Database: PDB / ID: 5x5g
TitleCrystal structure of TLA-3 extended-spectrum beta-lactamase in a complex with OP0595
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
Chem-OP0 / Beta-lactamase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionFeb 15, 2017Deposition 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 22, 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 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)31,9846
Polymers31,3471
Non-polymers6385
Water3,099172
1
A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,96912
Polymers62,6942
Non-polymers1,27510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4180 Å2
ΔGint-128 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.190, 67.910, 45.320
Angle α, β, γ (deg.)90.00, 94.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-499-

HOH

21A-523-

HOH

31A-538-

HOH

41A-549-

HOH

51A-551-

HOH

61A-554-

HOH

71A-572-

HOH

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Components

#1: Protein Beta-lactamase


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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-OP0 / (2S,5R)-N-(2-aminoethoxy)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide


Mass: 326.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H18N4O7S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.27 %
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: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2→55.22 Å / Num. obs: 18894 / % possible obs: 97 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 20
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 6.6 / Num. unique all: 2688 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GS8

5gs8


Resolution: 2→55.22 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.525 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 903 4.8 %RANDOM
Rwork0.16065 ---
obs0.16313 17989 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.633 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0.97 Å2
2---0.85 Å20 Å2
3---1.16 Å2
Refinement stepCycle: 1 / Resolution: 2→55.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 37 172 2380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192246
X-RAY DIFFRACTIONr_bond_other_d0.0010.022108
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9713036
X-RAY DIFFRACTIONr_angle_other_deg0.77534933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9535274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85626.19692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49115419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.13152
X-RAY DIFFRACTIONr_chiral_restr0.0980.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022416
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02404
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_it2.2471.8481099
X-RAY DIFFRACTIONr_mcbond_other2.2261.8451098
X-RAY DIFFRACTIONr_mcangle_it2.9152.7521372
X-RAY DIFFRACTIONr_mcangle_other2.9142.7551373
X-RAY DIFFRACTIONr_scbond_it3.5462.2131147
X-RAY DIFFRACTIONr_scbond_other3.5452.2141148
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9033.1721665
X-RAY DIFFRACTIONr_long_range_B_refined5.95523.392671
X-RAY DIFFRACTIONr_long_range_B_other5.95523.4012672
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 58 -
Rwork0.178 1310 -
obs--95.4 %

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