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- PDB-4gd8: SHV-1 beta-lactamase in complex with penam sulfone SA3-53 -

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Basic information

Entry
Database: PDB / ID: 4gd8
TitleSHV-1 beta-lactamase in complex with penam sulfone SA3-53
ComponentsBeta-lactamase SHV-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Class A beta-lactamase / hydrolase / 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 / Chem-MXF / Beta-lactamase SHV-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous replacement / Resolution: 1.6 Å
AuthorsPattanaik, P. / van den Akker, F.
CitationJournal: Plos One / Year: 2012
Title: Structures of SHV-1 beta-lactamase with penem and penam sulfone inhibitors that form cyclic intermediates stabilized by carbonyl conjugation
Authors: Ke, W. / Pattanaik, P. / Bethel, C.R. / Sheri, A. / Buynak, J.D. / Bonomo, R.A. / van den Akker, F.
History
DepositionJul 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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)32,7044
Polymers31,2601
Non-polymers1,4443
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.394, 55.460, 83.649
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
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-MXF / (2S,3R)-4-(2-aminoethylcarbamoyloxy)-2-[(2-methanoylindolizin-3-yl)amino]-3-methyl-3-sulfino-butanoic acid / penam sulfone SA3-53, open form


Mass: 426.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N4O7S
#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.: 152 / 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: 1.83 Å3/Da / Density % sol: 32.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% PEG 6000, 100mM HEPES pH7.0, 0.56mM Cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.979 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 24, 2005
RadiationMonochromator: Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→36.89 Å / Num. all: 29460 / Num. obs: 29342 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.3
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.5.0088refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: Isomorphous replacement / Resolution: 1.6→36.89 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.315 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1556 5 %RANDOM
Rwork0.19774 ---
obs0.19993 29342 99.61 %-
all-29456 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.243 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→36.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 73 152 2249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222167
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7412.0052942
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1915273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92623.07791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26515369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3861524
X-RAY DIFFRACTIONr_chiral_restr0.1120.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211596
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_it3.1531.51339
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.09222150
X-RAY DIFFRACTIONr_scbond_it7.1323828
X-RAY DIFFRACTIONr_scangle_it9.4544.5788
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 110 -
Rwork0.33 2141 -
obs--99.38 %

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