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- PDB-4zj3: Crystal structure of cephalexin bound acyl-enzyme intermediate of... -

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Basic information

Entry
Database: PDB / ID: 4zj3
TitleCrystal structure of cephalexin bound acyl-enzyme intermediate of Val216AcrF mutant TEM1 beta-lactamase from Escherichia coli: E166N and V216AcrF 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsXiao, H. / Nasertorabi, F. / Choi, S. / Han, G.W. / Reed, S.A. / Stevens, R.C. / 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 29, 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)33,3281
Polymers33,3281
Non-polymers00
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.290, 47.025, 128.309
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: 33328.117 Da / Num. of mol.: 1 / Mutation: E166N,V216AcrF
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.: 307 / 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: 41.29 %
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: BL7-1 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.7→37.93 Å / Num. obs: 31711 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 15.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

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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: 1.7→25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.323 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18838 1593 5 %RANDOM
Rwork0.15387 ---
obs0.15566 30049 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2--0.18 Å2-0 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 0 307 2375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192222
X-RAY DIFFRACTIONr_bond_other_d0.0040.022137
X-RAY DIFFRACTIONr_angle_refined_deg1.9221.9933025
X-RAY DIFFRACTIONr_angle_other_deg1.5863.0044923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3495.071281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.07523.69692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82915380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1811519
X-RAY DIFFRACTIONr_chiral_restr0.1120.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212574
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02500
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_it0.7881.2061116
X-RAY DIFFRACTIONr_mcbond_other0.7891.2041114
X-RAY DIFFRACTIONr_mcangle_it1.251.8071409
X-RAY DIFFRACTIONr_mcangle_other1.251.8091410
X-RAY DIFFRACTIONr_scbond_it1.4791.4221106
X-RAY DIFFRACTIONr_scbond_other1.4781.4231107
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4152.0611617
X-RAY DIFFRACTIONr_long_range_B_refined4.15812.24710343
X-RAY DIFFRACTIONr_long_range_B_other3.84911.75210008
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 117 -
Rwork0.232 2198 -
obs--99.74 %
Refinement TLS params.Method: refined / Origin x: -8.0573 Å / Origin y: 10.8096 Å / Origin z: -15.5225 Å
111213212223313233
T0.0359 Å20.0014 Å20.0086 Å2-0.0102 Å20.0043 Å2--0.007 Å2
L0.2287 °20.0159 °2-0.0235 °2-0.4558 °20.3903 °2--0.3894 °2
S0.0224 Å °0.0285 Å °0.0026 Å °0.0363 Å °-0.0388 Å °0.0019 Å °0.0267 Å °-0.0264 Å °0.0164 Å °

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