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- PDB-4zj1: Crystal Structure of p-acrylamido-phenylalanine modified TEM1 bet... -

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Basic information

Entry
Database: PDB / ID: 4zj1
TitleCrystal Structure of p-acrylamido-phenylalanine modified TEM1 beta-lactamase from Escherichia coli : 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 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
DI(HYDROXYETHYL)ETHER / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 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 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jul 20, 2016Group: Data collection
Revision 1.3Sep 27, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3894
Polymers32,9961
Non-polymers3933
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.470, 47.240, 128.330
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: 32995.734 Da / Num. of mol.: 1 / Mutation: 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.09 Å3/Da / Density % sol: 41.11 %
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: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Sep 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→26.54 Å / Num. obs: 41549 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 16.3
Reflection shellResolution: 1.54→1.63 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 6.5 / % 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: 1.54→25 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.077 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17045 2082 5 %RANDOM
Rwork0.14035 ---
obs0.14185 39324 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.414 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å20 Å2
2---0.52 Å20 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 1.54→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 25 468 2543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192291
X-RAY DIFFRACTIONr_bond_other_d0.0030.022214
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9843116
X-RAY DIFFRACTIONr_angle_other_deg1.0435110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6785.034298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.67823.93999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67315401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9911520
X-RAY DIFFRACTIONr_chiral_restr0.2520.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212651
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02508
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_it1.3962.2791154
X-RAY DIFFRACTIONr_mcbond_other1.3542.271153
X-RAY DIFFRACTIONr_mcangle_it2.0844.2631467
X-RAY DIFFRACTIONr_mcangle_other2.094.2741468
X-RAY DIFFRACTIONr_scbond_it2.6752.921137
X-RAY DIFFRACTIONr_scbond_other2.6742.921137
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.025.1841650
X-RAY DIFFRACTIONr_long_range_B_refined7.4217.4363177
X-RAY DIFFRACTIONr_long_range_B_other7.41917.4413178
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.54→1.584 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 167 -
Rwork0.194 2848 -
obs--99.87 %
Refinement TLS params.Method: refined / Origin x: -7.8798 Å / Origin y: 11.2073 Å / Origin z: -15.4523 Å
111213212223313233
T0.0153 Å20.0038 Å20.0035 Å2-0.0074 Å2-0.0026 Å2--0.0043 Å2
L0.0811 °20.0004 °2-0.0408 °2-0.1905 °20.1494 °2--0.2169 °2
S0.0107 Å °0.0067 Å °-0.0066 Å °-0.0162 Å °-0.014 Å °-0.0047 Å °-0.0155 Å °-0.0058 Å °0.0033 Å °

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