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- PDB-1rcj: Crystal structure of E166A mutant of SHV-1 beta-lactamase with th... -

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Basic information

Entry
Database: PDB / ID: 1rcj
TitleCrystal structure of E166A mutant of SHV-1 beta-lactamase with the trans-enamine intermediate of tazobactam
ComponentsBeta-lactamase SHV-1
KeywordsHYDROLASE / BETA-LACTAMASE / BETA-LACTAM HYDROLASE / PENICILLINASE / DETERGENT BINDING / INHIBITOR DESIGN / COVALENT INTERMEDIATE
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
CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE / TAZOBACTAM TRANS-ENAMINE INTERMEDIATE / Beta-lactamase SHV-1 / Beta-lactamase SHV-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsPadayatti, P.S. / Helfand, M.S. / Totir, M.A. / Carey, M.P. / Hujer, A.M. / Carey, P.R. / Bonomo, R.A. / van den Akker, F.
CitationJournal: Biochemistry / Year: 2004
Title: Tazobactam Forms a Stoichiometric trans-Enamine Intermediate in the E166A Variant of SHV-1 beta-Lactamase: 1.63 A Crystal Structure
Authors: Padayatti, P.S. / Helfand, M.S. / Totir, M.A. / Carey, M.P. / Hujer, A.M. / Carey, P.R. / Bonomo, R.A. / Van Den Akker, F.
History
DepositionNov 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 13, 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 SHV-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1684
Polymers28,8491
Non-polymers1,3203
Water5,405300
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.848, 55.193, 83.733
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase SHV-1 / PIT-2


Mass: 28848.982 Da / Num. of mol.: 1 / Mutation: E166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: BLA, SHV1 / Production host: Escherichia coli (E. coli)
References: UniProt: P14557, UniProt: P0AD64*PLUS, beta-lactamase
#2: Chemical ChemComp-MA4 / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE


Mass: 508.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H44O11
#3: Chemical ChemComp-TBI / TAZOBACTAM TRANS-ENAMINE INTERMEDIATE


Mass: 302.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N4O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystal was soaked for 20 minutes in mother liquor containing 5mM Tazobactam prior to flash freezing. 30% PEG 6000, 0.1M HEPES, 0.56mM Cymal-6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15.6 mMCymal-61drop
230 %(w/v)PEG60001drop
30.1 MHEPES1droppH7.0
430 %(w/v)PEG60001reservoir
50.1 MHEPES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2003 / Details: Yale mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→30 Å / Num. all: 29632 / Num. obs: 28328 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 11.8 Å2 / Rsym value: 0.032 / Net I/σ(I): 40.5
Reflection shellResolution: 1.63→1.69 Å / Rsym value: 0.08 / % possible all: 87.7
Reflection
*PLUS
Rmerge(I) obs: 0.032
Reflection shell
*PLUS
% possible obs: 87.7 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 12.6

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G56

1g56
PDB Unreleased entry


Resolution: 1.63→30 Å / Isotropic thermal model: Overall anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.171 1372 -random
Rwork0.147 ---
all-29531 --
obs-28279 95.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--1.643 Å20 Å2
3----1.203 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.161 Å0.134 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.039 Å
Refinement stepCycle: LAST / Resolution: 1.63→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2064 0 64 300 2428
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0088
X-RAY DIFFRACTIONc_angle_d1.578
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.58

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