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- PDB-4jpm: Structure of SHV-1 beta-lactamase in complex with the 7-alkyliden... -

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Basic information

Entry
Database: PDB / ID: 4jpm
TitleStructure of SHV-1 beta-lactamase in complex with the 7-alkylidenecephalosporin DCM-1-10 at 1.14 Ang resolution
ComponentsBeta-lactamase SHV-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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
7-alkylidenecephalosporin DCM-1-10, bound form / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE / Beta-lactamase SHV-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsRodkey, E.A. / van den Akker, F.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: beta-Lactamase Inhibition by 7-Alkylidenecephalosporin Sulfones: Allylic Transposition and Formation of an Unprecedented Stabilized Acyl-Enzyme.
Authors: Rodkey, E.A. / McLeod, D.C. / Bethel, C.R. / Smith, K.M. / Xu, Y. / Chai, W. / Che, T. / Carey, P.R. / Bonomo, R.A. / van den Akker, F. / Buynak, J.D.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Sep 20, 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_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 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)32,9195
Polymers31,2601
Non-polymers1,6594
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.308, 55.222, 84.285
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: 31259.988 Da / Num. of mol.: 1 / Fragment: SVH-1 beta-lactamase
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-1OG / 7-alkylidenecephalosporin DCM-1-10, bound form / (3Z,5Z,7S,8R)-3-[(acetyloxy)methyl]-8-(tert-butoxycarbonyl)-7-formyl-7,8-dihydro-2H-1,5-thiazocine-4-carboxylic acid 1,1-dioxide


Mass: 403.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21NO9S
#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.: 338 / 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: 1.84 Å3/Da / Density % sol: 32.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 21-30% PEG 6000, 0.1M HEPES buffer, 0.56mM Cymal-6, pH 6.8-7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
PH range: 6.8-7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2010
RadiationMonochromator: Monochr. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.14→24.41 Å / Num. all: 79862 / Num. obs: 76013 / % possible obs: 95.18 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 13.8
Reflection shellResolution: 1.14→1.18 Å / Redundancy: 3.2 % / Rsym value: 0.351 / % possible all: 77.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1SHV

1shv


Resolution: 1.14→24.41 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.018 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16362 3993 5 %RANDOM
Rwork0.13054 ---
obs0.13223 76013 95.18 %-
all-79862 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.605 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.14→24.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 77 338 2439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222262
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4592.0093081
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9995291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91723.40494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94115387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6381523
X-RAY DIFFRACTIONr_chiral_restr0.0870.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211687
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9451.51398
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.86122254
X-RAY DIFFRACTIONr_scbond_it6.0573864
X-RAY DIFFRACTIONr_scangle_it8.2684.5827
X-RAY DIFFRACTIONr_rigid_bond_restr3.63832262
X-RAY DIFFRACTIONr_sphericity_free18.7023338
X-RAY DIFFRACTIONr_sphericity_bonded9.08632216
LS refinement shellResolution: 1.142→1.172 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 247 -
Rwork0.233 4768 -
obs--81.66 %

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