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- PDB-4zj2: Crystal Structure of p-acrylamido-phenylalanine modified TEM1 bet... -

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Basic information

Entry
Database: PDB / ID: 4zj2
TitleCrystal Structure of p-acrylamido-phenylalanine modified TEM1 beta-lactamase from Escherichia coli :E166N mutant
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / noncanonical amino acid / beta-lactamase / protein evolution / evolutionary advantage
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsXiao, H. / Nasertorabi, F. / Choi, S. / Han, G.W. / Reed, S.A. / Stevens, C.S. / Schultz, P.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Exploring the potential impact of an expanded genetic code on protein function.
Authors: Xiao, H. / Nasertorabi, F. / Choi, S.H. / Han, G.W. / Reed, S.A. / Stevens, R.C. / Schultz, P.G.
History
DepositionApr 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)33,2111
Polymers33,2111
Non-polymers00
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.461, 47.044, 127.580
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 / 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: 33211.012 Da / Num. of mol.: 1 / Mutation: E166N
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS USED THE SEQUENCE FROM NCBI REFERENCE SEQUENCE: WP_000027050.1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1M 2-(N-morpholino) ethanesulfonic acid (MES) pH 6.5, 15% PEG 20.000 and 15% PEG 550MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→37.86 Å / Num. obs: 26744 / % possible obs: 100 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 15
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BTL

1btl


Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.667 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20904 1343 5 %RANDOM
Rwork0.16529 ---
obs0.16753 25336 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.712 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--1.14 Å2-0 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 0 213 2275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192153
X-RAY DIFFRACTIONr_bond_other_d0.0030.022081
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.9792925
X-RAY DIFFRACTIONr_angle_other_deg1.183.0044788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0125.037273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.723.97893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17615374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1181518
X-RAY DIFFRACTIONr_chiral_restr0.1320.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212458
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02473
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_it1.8013.3351087
X-RAY DIFFRACTIONr_mcbond_other1.7823.331086
X-RAY DIFFRACTIONr_mcangle_it2.3826.2271364
X-RAY DIFFRACTIONr_mcangle_other2.3936.2321365
X-RAY DIFFRACTIONr_scbond_it3.8754.2051066
X-RAY DIFFRACTIONr_scbond_other3.8734.2071067
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.777.4721562
X-RAY DIFFRACTIONr_long_range_B_refined6.28221.3029998
X-RAY DIFFRACTIONr_long_range_B_other6.20921.0169815
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 85 -
Rwork0.246 1833 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -8.0296 Å / Origin y: 10.6447 Å / Origin z: -15.4196 Å
111213212223313233
T0.0367 Å20.0092 Å20.0027 Å2-0.0349 Å2-0.0005 Å2--0.0093 Å2
L0.2557 °20.0341 °20.118 °2-0.5184 °20.4227 °2--0.4674 °2
S0.0348 Å °0.0259 Å °0.0014 Å °0.0557 Å °-0.0523 Å °-0.0035 Å °0.0263 Å °-0.0497 Å °0.0175 Å °

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