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- PDB-1fqg: MOLECULAR STRUCTURE OF THE ACYL-ENZYME INTERMEDIATE IN TEM-1 BETA... -

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Basic information

Entry
Database: PDB / ID: 1fqg
TitleMOLECULAR STRUCTURE OF THE ACYL-ENZYME INTERMEDIATE IN TEM-1 BETA-LACTAMASE
ComponentsTEM-1 BETA-LACTAMASE
KeywordsHYDROLASE / beta-lactamase / acyl-enzyme / penicillin / class A
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
OPEN FORM - PENICILLIN G / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsStrynadka, N.C.
CitationJournal: Nature / Year: 1992
Title: Molecular structure of the acyl-enzyme intermediate in beta-lactam hydrolysis at 1.7 A resolution.
Authors: Strynadka, N.C. / Adachi, H. / Jensen, S.E. / Johns, K. / Sielecki, A. / Betzel, C. / Sutoh, K. / James, M.N.
History
DepositionSep 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TEM-1 BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2632
Polymers28,9271
Non-polymers3361
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.2, 88.3, 41.6
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TEM-1 BETA-LACTAMASE


Mass: 28926.982 Da / Num. of mol.: 1 / Mutation: GLU166ASN MUTATION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PHA508 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-PNM / OPEN FORM - PENICILLIN G


Mass: 336.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N2O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.97 Å3/Da / Density % sol: 37.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.4M sodium potassium phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: other / Details: used macroseeding
Components of the solutions
*PLUS
Conc.: 1.4 M / Common name: sodium potassium phosphate / Details: pH8

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.009
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1992
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.7→10 Å / Num. all: 88517 / Num. obs: 24067 / % possible obs: 92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.2
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.106 / Num. unique all: 1622 / % possible all: 82.9
Reflection
*PLUS
Rmerge(I) obs: 0.22

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Processing

Software
NameVersionClassification
MAR345data collection
ROTAVATAdata reduction
MLPHAREphasing
TNTrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 1.7→10 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: prolsq
RfactorNum. reflection% reflectionSelection details
Rwork0.182 ---
all0.182 24067 --
obs0.182 24067 92 %-
Rfree-0 -0
Solvent computationSolvent model: TNT / Bsol: 216.069 Å2 / ksol: 1.13506 e/Å3
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 23 150 2198
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00620861
X-RAY DIFFRACTIONt_angle_deg1.58728151.5
X-RAY DIFFRACTIONt_dihedral_angle_d15.73412580
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_trig_c_planes0.007531.5
X-RAY DIFFRACTIONt_gen_planes0.0123003.5
X-RAY DIFFRACTIONt_it1.43720870.3
X-RAY DIFFRACTIONt_nbd0.0451512
Refinement
*PLUS
Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0161
X-RAY DIFFRACTIONt_angle_deg3.11.5
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.7340
X-RAY DIFFRACTIONt_planar_d0.0071.5
X-RAY DIFFRACTIONt_plane_restr0.0123.5

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