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- PDB-3cmz: TEM-1 Class-A beta-lactamase L201P mutant apo structure -

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Basic information

Entry
Database: PDB / ID: 3cmz
TitleTEM-1 Class-A beta-lactamase L201P mutant apo structure
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / stabilization mutation / Antibiotic resistance / Plasmid / Transposable element
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
PHOSPHATE ION / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsMarciano, D.C. / Wang, X. / Wang, J. / Chen, Y. / Thomas, V.L. / Shoichet, B.K. / Palzkill, T.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Genetic and structural characterization of an L201P global suppressor substitution in TEM-1 beta-lactamase
Authors: Marciano, D.C. / Pennington, J.M. / Wang, X. / Wang, J. / Chen, Y. / Thomas, V.L. / Shoichet, B.K. / Palzkill, T.
History
DepositionMar 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / 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 / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0212
Polymers28,9261
Non-polymers951
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.218, 59.140, 87.802
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 28925.951 Da / Num. of mol.: 1 / Mutation: L201P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Plasmid: pBG66 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 1.85 Å3/Da / Density % sol: 33.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.6M potassium phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11591 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 10, 2006 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11591 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. all: 16966 / Num. obs: 15609 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 25.8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 14
Reflection shellResolution: 1.92→1.99 Å / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.48 / Num. unique all: 1386 / % possible all: 83.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JWP

1jwp


Resolution: 1.92→49.03 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.186 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2421 787 5 %RANDOM
Rwork0.19552 ---
all0.19787 15609 --
obs0.19787 14801 91.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.9 Å2
Refinement stepCycle: LAST / Resolution: 1.92→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 5 123 2154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222066
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9782801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6645262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24923.8289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17715364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8441518
X-RAY DIFFRACTIONr_chiral_restr0.0960.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021545
X-RAY DIFFRACTIONr_nbd_refined0.2070.21041
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21455
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2134
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.210
X-RAY DIFFRACTIONr_mcbond_it0.8741.51342
X-RAY DIFFRACTIONr_mcangle_it1.42222102
X-RAY DIFFRACTIONr_scbond_it2.253808
X-RAY DIFFRACTIONr_scangle_it3.5154.5699
LS refinement shellResolution: 1.92→1.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 49 -
Rwork0.222 931 -
obs-931 79.55 %

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