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- PDB-3oph: ESBL R164S mutant of SHV-1 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 3oph
TitleESBL R164S mutant of SHV-1 beta-lactamase
ComponentsBeta-lactamase SHV-1
KeywordsHYDROLASE / Class A beta-lactamase
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 / Beta-lactamase SHV-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.34 Å
AuthorsSampson, J.M. / van den Akker, F.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2011
Title: Ligand-dependent disorder of the Omega loop observed in extended-spectrum SHV-type beta-lactamase.
Authors: Sampson, J.M. / Ke, W. / Bethel, C.R. / Pagadala, S.R. / Nottingham, M.D. / Bonomo, R.A. / Buynak, J.D. / van den Akker, F.
History
DepositionSep 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 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 / pdbx_initial_refinement_model / 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 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase SHV-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4454
Polymers31,1901
Non-polymers1,2563
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.777, 55.635, 83.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer in asymmetric unit

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Components

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


Mass: 31189.875 Da / Num. of mol.: 1 / Mutation: R164S
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: P0AD64, 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-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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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

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Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 21-30% PEG 6000, 0.5mM cymal-6, 100mM HEPES buffer, pH 6.6-7.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K
PH range: 6.6-7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2006
RadiationMonochromator: a vertically focusing mirror and a horizontally focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. all: 52100 / Num. obs: 51631 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.8
Reflection shellResolution: 1.34→1.39 Å / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 4.9 / % possible all: 94.6

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Processing

Software
NameClassification
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1VM1

1vm1


Resolution: 1.34→31.79 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.788 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18994 2625 5.1 %RANDOM
Rwork0.16191 ---
obs0.1633 48954 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.205 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.34→31.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 61 341 2421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222228
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9993033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0165291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60522.91796
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3915389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9471526
X-RAY DIFFRACTIONr_chiral_restr0.0820.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211650
X-RAY DIFFRACTIONr_mcbond_it1.5751.51372
X-RAY DIFFRACTIONr_mcangle_it2.37222208
X-RAY DIFFRACTIONr_scbond_it4.1463856
X-RAY DIFFRACTIONr_scangle_it6.184.5814
LS refinement shellResolution: 1.34→1.376 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 186 -
Rwork0.233 3487 -
obs--97.66 %

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