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- PDB-4op8: Room temperature crystal structure of stabilized TEM-1 beta-lacta... -

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Basic information

Entry
Database: PDB / ID: 4op8
TitleRoom temperature crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying G238S mutation
ComponentsTEM-94 ES-beta-lactamase
KeywordsHYDROLASE / Beta-Lactamase
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDellus-Gur, E. / Elias, M. / Fraser, J.S. / Tawfik, D.S.
CitationJournal: J. Mol. Biol. / Year: 2015
Title: Negative Epistasis and Evolvability in TEM-1 beta-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder.
Authors: Dellus-Gur, E. / Elias, M. / Caselli, E. / Prati, F. / Salverda, M.L. / de Visser, J.A. / Fraser, J.S. / Tawfik, D.S.
History
DepositionFeb 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 20, 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 / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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: TEM-94 ES-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1314
Polymers28,8011
Non-polymers3303
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TEM-94 ES-beta-lactamase
hetero molecules

A: TEM-94 ES-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2628
Polymers57,6022
Non-polymers6616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area2280 Å2
ΔGint-71 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.360, 47.040, 34.920
Angle α, β, γ (deg.)90.00, 92.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TEM-94 ES-beta-lactamase


Mass: 28800.807 Da / Num. of mol.: 1 / Fragment: TEM-1
Mutation: G238S, A42G, N52A, I84V, R120G, M182T, L201A, T265M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla-TEM-94 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KMX3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 9% (wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES pH 6.2, and 200mM Ca(OAc)2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.75→77.36 Å / Num. all: 80712 / Num. obs: 16253 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ZG4

1zg4


Resolution: 1.95→44.99 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.281 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23016 856 5 %RANDOM
Rwork0.17691 ---
obs0.17951 16253 92.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.703 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å2-0 Å2
2--0.21 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.95→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 19 146 2182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0192244
X-RAY DIFFRACTIONr_bond_other_d0.0010.022197
X-RAY DIFFRACTIONr_angle_refined_deg0.691.9853077
X-RAY DIFFRACTIONr_angle_other_deg0.5133.0015103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0715316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.01924.257101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0715417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3781519
X-RAY DIFFRACTIONr_chiral_restr0.0430.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212576
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02485
X-RAY DIFFRACTIONr_mcbond_it2.7092.3711107
X-RAY DIFFRACTIONr_mcbond_other2.7082.371106
X-RAY DIFFRACTIONr_mcangle_it4.0373.5521396
X-RAY DIFFRACTIONr_mcangle_other4.0363.5521397
X-RAY DIFFRACTIONr_scbond_it3.4632.8071137
X-RAY DIFFRACTIONr_scbond_other3.4582.8041133
X-RAY DIFFRACTIONr_scangle_other5.2694.0611648
X-RAY DIFFRACTIONr_long_range_B_refined8.1920.0162724
X-RAY DIFFRACTIONr_long_range_B_other8.09319.7482687
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 60 -
Rwork0.233 1134 -
obs--90.11 %

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