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- PDB-4fd8: Structure of apo S70C SHV beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 4fd8
TitleStructure of apo S70C SHV beta-lactamase
ComponentsBeta-lactamase SHV-1
KeywordsHYDROLASE / class A beta-lactamase / hydrolase-hydrolase inhibitor complex
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 / MIR / Resolution: 1.52 Å
AuthorsRodkey, E.A. / van den Akker, F.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Crystal structure of a pre-acylation complex of the beta-lactamase inhibitor, sulbactam, bound to a sulfenamide bond containing thiol-beta-lactamase
Authors: Rodkey, E.A. / Drawz, S.M. / Sampson, J.M. / Bethel, C.R. / Bonomo, R.A. / van den Akker, F.
History
DepositionMay 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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)29,9403
Polymers28,9231
Non-polymers1,0172
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.354, 55.584, 84.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 28923.084 Da / Num. of mol.: 1 / Fragment: unp residues 22-286 / Mutation: S70C
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O

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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: 38.55 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 21-30% PEG6k, 0.1M hepes pH 6.8-7.8, 0.56mM cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 296K
PH range: 6.8-7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 13, 2009
RadiationMonochromator: Double crystal monochromator, Rh coated flat mirror, toroidal focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. all: 36725 / Num. obs: 35770 / % possible obs: 97.4 % / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0110phasing
RefinementMethod to determine structure: MIR / Resolution: 1.52→27.78 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.402 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19702 1782 5 %RANDOM
Rwork0.16604 ---
all0.16764 34951 --
obs0.16764 33962 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.152 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.52→27.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 42 272 2338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212214
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.993011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3215288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42223.01193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09715387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3781525
X-RAY DIFFRACTIONr_chiral_restr0.0920.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211657
X-RAY DIFFRACTIONr_mcbond_it0.7611.51391
X-RAY DIFFRACTIONr_mcangle_it1.36822240
X-RAY DIFFRACTIONr_scbond_it2.3633823
X-RAY DIFFRACTIONr_scangle_it3.8474.5771
LS refinement shellResolution: 1.516→1.555 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 91 -
Rwork0.252 2089 -
obs--81.1 %

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