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- PDB-2h0t: Crystal structure of the M69V E166A double mutant of SHV-1 b-lact... -

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Basic information

Entry
Database: PDB / ID: 2h0t
TitleCrystal structure of the M69V E166A double mutant of SHV-1 b-lactamase complexed to clavulanic acid
ComponentsBroad-spectrum beta-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 / Chem-TEM / Beta-lactamase SHV-1 / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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_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_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 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: Broad-spectrum beta-lactamase SHV-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2305
Polymers28,8171
Non-polymers1,4134
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.680, 55.200, 83.490
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 Broad-spectrum beta-lactamase SHV-1 / Extended-spectrum beta-lactamase SHV-11 / SHV type extended spectrum beta-lactamase / Bla-SHV type 1


Mass: 28816.920 Da / Num. of mol.: 1 / Fragment: SHV-1 b-lactamase / Mutation: M69V, E166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaSHV-1, SHV-1b-a, blaSHV-11 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5PSW7, UniProt: P0AD64*PLUS, beta-lactamase
#2: Chemical ChemComp-TEM / N-(2-HYDROXY-4-OXO-BUTYL)-N-(3-OXO-TRANSPROPENYL)AMINE


Mass: 157.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO3
#3: Chemical ChemComp-MA4 / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE


Mass: 508.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H44O11
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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 pH 7.0, 0.56mM Cymal-6. Crystal is soaked for 10 minutes in 50mM clavulanic acid prior to freezing and data collection., 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: 1.6→19.91 Å / Num. obs: 31000 / % possible obs: 95.1 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Biso Wilson estimate: 16.7 Å2 / Rsym value: 0.094 / Net I/σ(I): 9.8
Reflection shellResolution: 1.6→1.66 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.506 / % possible all: 90.9

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Processing

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

1rcj


Resolution: 1.6→18.53 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1331953.67 / Data cutoff high rms absF: 1331953.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2936 10 %RANDOM
Rwork0.16 ---
obs0.16 29420 94.9 %-
all-31000 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.2699 Å2 / ksol: 0.454706 e/Å3
Displacement parametersBiso mean: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2---1.57 Å20 Å2
3---0.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→18.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 61 269 2384
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d1.04
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 449 9.7 %
Rwork0.224 4181 -
obs--91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3clav_decarbox.parnew_ligands4.top
X-RAY DIFFRACTION4new_cymal.parion.top
X-RAY DIFFRACTION5hepes.par

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