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- PDB-2h10: Crystal structure of the M69V E166A double mutant of SHV-1 b-lact... -

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Basic information

Entry
Database: PDB / ID: 2h10
TitleCrystal structure of the M69V E166A double mutant of SHV-1 b-lactamase complexed to tazobactam
ComponentsBeta-lactamase SHV-1
KeywordsHYDROLASE / antibiotic resistance / b-lactamase inhibitor
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 INTERMEDIATE / Beta-lactamase SHV-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
Authorsvan den Akker, F. / Padayatti, P.S.
CitationJournal: Biochemistry / Year: 2006
Title: Effect of the inhibitor-resistant M69V substitution on the structures and populations of trans-enamine beta-lactamase intermediates.
Authors: Totir, M.A. / Padayatti, P.S. / Helfand, M.S. / Carey, M.P. / Bonomo, R.A. / Carey, P.R. / van den Akker, F.
History
DepositionMay 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 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 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 20, 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)30,1364
Polymers28,8171
Non-polymers1,3203
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.670, 55.180, 83.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsprotein is a monomer

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Components

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


Mass: 28816.920 Da / Num. of mol.: 1 / Mutation: M69V, E166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, shv1 / Plasmid: pBC SK(-) / Species (production host): Escherichia coli
Production host: Escherichia coli str. K-12 substr. DH10B (bacteria)
Strain (production host): DH10B / References: UniProt: P0AD64, beta-lactamase
#2: Chemical ChemComp-TBE / TAZOBACTAM INTERMEDIATE


Mass: 302.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N4O5S
#3: Chemical ChemComp-MA4 / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE


Mass: 508.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H44O11
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 1.99 Å3/Da / Density % sol: 38.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 6000, 0.1M HEPES, 0.56mM Cymal-6. Crystal soaked for 10 minutes in 50mM tazobactam prior to freezing and data collection, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.46 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Sep 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.46 Å / Relative weight: 1
ReflectionResolution: 1.75→19.91 Å / Num. obs: 23825 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.059
Reflection shellResolution: 1.75→1.81 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.299 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RCJ

1rcj


Resolution: 1.75→19.91 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1358824.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2349 9.9 %RANDOM
Rwork0.159 ---
all0 0 --
obs0.159 23773 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.9669 Å2 / ksol: 0.40075 e/Å3
Displacement parametersBiso mean: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å20 Å20 Å2
2---3.27 Å20 Å2
3---0.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.75→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 64 307 2425
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d1.03
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 373 9.5 %
Rwork0.251 3534 -
obs-3534 99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3prodr_tazo4.parnew_ligands.top
X-RAY DIFFRACTION4new_cymal.parion.top

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