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- PDB-4mez: Crystal structure of M68L/M69T double mutant TEM-1 -

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Basic information

Entry
Database: PDB / ID: 4mez
TitleCrystal structure of M68L/M69T double mutant TEM-1
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.047 Å
AuthorsPark, J. / Gobeil, S. / Pelletier, J.N. / Berghuis, A.M.
CitationJournal: Sci Rep / Year: 2019
Title: The Structural Dynamics of Engineered beta-Lactamases Vary Broadly on Three Timescales yet Sustain Native Function.
Authors: Gobeil, S.M.C. / Ebert, M.C.C.J.C. / Park, J. / Gagne, D. / Doucet, N. / Berghuis, A.M. / Pleiss, J. / Pelletier, J.N.
History
DepositionAug 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _struct_ref_seq_dif.details
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 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 TEM
B: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2398
Polymers57,7882
Non-polymers4516
Water6,233346
1
A: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2145
Polymers28,8941
Non-polymers3204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0253
Polymers28,8941
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.333, 55.071, 77.681
Angle α, β, γ (deg.)70.83, 81.22, 71.84
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999997, 0.000134, 0.00251), (0.000132, -1, 0.000533), (0.00251, -0.000533, -0.999997)17.11922, 59.6031, 24.55211

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Components

#1: Protein Beta-lactamase TEM / IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 ...IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2


Mass: 28893.865 Da / Num. of mol.: 2 / Mutation: M66L, M67T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 10, 2012 / Details: VariMax HF
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.047→73.26 Å / Num. all: 31963 / Num. obs: 31707 / % possible obs: 99.2 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 11.8
Reflection shellResolution: 2.047→2.09 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1521 / % possible all: 97.2

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASER2.1.4phasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZG4

1zg4


Resolution: 2.047→73.26 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.887 / SU B: 4.603 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 1607 5.1 %RANDOM
Rwork0.19211 ---
all0.19495 30099 --
obs0.19495 30099 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.363 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.09 Å20.21 Å2
2--0.12 Å2-0.24 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.047→73.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 23 346 4369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194161
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.9775663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9855538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41823.864176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53815704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.541535
X-RAY DIFFRACTIONr_chiral_restr0.1330.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213129
LS refinement shellResolution: 2.047→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 124 -
Rwork0.189 2039 -
obs-2163 91.69 %

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