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- PDB-4oqi: Crystal structure of stabilized TEM-1 beta-lactamase variant v.13... -

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Basic information

Entry
Database: PDB / ID: 4oqi
TitleCrystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S/G238S mutations
ComponentsTEM-94 ES-beta-lactamase
Keywordshydrolase/hydrolase inhibitor / Beta-lctamase / hydrolase-hydrolase inhibitor complex
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 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 9, 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 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_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

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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)28,8673
Polymers28,7311
Non-polymers1362
Water6,792377
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)57,7346
Polymers57,4612
Non-polymers2724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1360 Å2
ΔGint-44 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.930, 46.400, 34.430
Angle α, β, γ (deg.)90.00, 93.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-301-

CA

21A-726-

HOH

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Components

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


Mass: 28730.689 Da / Num. of mol.: 1 / Fragment: TEM-1
Mutation: G238S, R164S, 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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 293 K / pH: 6.2
Details: 9% (wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES, and 200mM Ca(OAc)2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.973
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.13→38.24 Å / Num. obs: 82624 / Observed criterion σ(I): 3 / Redundancy: 3.57 % / Rsym value: 0.063 / Net I/σ(I): 11.98
Reflection shellResolution: 1.13→1.2 Å / Redundancy: 3.18 % / Mean I/σ(I) obs: 4.46 / Rsym value: 0.199 / % possible all: 85.7

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→44.4 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.935 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.155 4132 5 %RANDOM
Rwork0.122 ---
obs0.124 78491 91.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å20.31 Å2
2--0.23 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.13→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 6 377 2395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192302
X-RAY DIFFRACTIONr_bond_other_d0.0010.022247
X-RAY DIFFRACTIONr_angle_refined_deg2.1811.9813158
X-RAY DIFFRACTIONr_angle_other_deg1.1953.0015208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7355322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60123.9100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66115425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4781520
X-RAY DIFFRACTIONr_chiral_restr0.1590.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212668
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02504
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_it4.0981.171158
X-RAY DIFFRACTIONr_mcbond_other4.11.171157
X-RAY DIFFRACTIONr_mcangle_it4.9521.7661467
X-RAY DIFFRACTIONr_mcangle_other4.9511.7661468
X-RAY DIFFRACTIONr_scbond_it5.2141.5541144
X-RAY DIFFRACTIONr_scbond_other5.2121.5531140
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8712.2131665
X-RAY DIFFRACTIONr_long_range_B_refined7.63312.5943178
X-RAY DIFFRACTIONr_long_range_B_other7.23610.9682853
X-RAY DIFFRACTIONr_rigid_bond_restr8.64834549
X-RAY DIFFRACTIONr_sphericity_free32.003553
X-RAY DIFFRACTIONr_sphericity_bonded15.53754839
LS refinement shellResolution: 1.13→1.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 282 -
Rwork0.182 5344 -
obs--84.77 %

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