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- PDB-3v50: Complex of SHV S130G mutant beta-lactamase complexed to SA2-13 -

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Basic information

Entry
Database: PDB / ID: 3v50
TitleComplex of SHV S130G mutant beta-lactamase complexed to SA2-13
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / class A beta-lactamase fold / hydrolyze b-lactam antibiotics / 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-SA2 / Beta-lactamase SHV-1 / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsWei, K. / van den Akker, F.
CitationJournal: Chemmedchem / Year: 2012
Title: The importance of the trans-enamine intermediate as a beta-lactamase inhibition strategy probed in inhibitor-resistant SHV beta-lactamase variants.
Authors: Ke, W. / Rodkey, E.A. / Sampson, J.M. / Skalweit, M.J. / Sheri, A. / Pagadala, S.R. / Nottingham, M.D. / Buynak, J.D. / Bonomo, R.A. / van den Akker, F.
History
DepositionDec 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 27, 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_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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2604
Polymers28,8771
Non-polymers1,3833
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.671, 55.479, 83.620
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 / Beta-lactamase SHV-1 / Beta-lactamase bla-SHV-1 / Beta-lactamase blaSHV-1 / Bla-SHV type 1 / Broad- ...Beta-lactamase SHV-1 / Beta-lactamase bla-SHV-1 / Beta-lactamase blaSHV-1 / Bla-SHV type 1 / Broad-spectrum beta-lactamase SHV-1 / Extended-spectrum beta-lactamase SHV-11 / SHV type beta lactamase / SHV type extended spectrum beta-lactamase / SHV-1 beta-lactamase


Mass: 28876.994 Da / Num. of mol.: 1 / Fragment: SHV-1 beta-lactamase / Mutation: S130G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: blaSHV-1, blaCTX-M, blaSHV, blaSHV-11, blaSHV1, SHV, shv-1, SHV-1, SHV-1b-a
Plasmid: PBC SK(-) / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 substr.DH10B
References: UniProt: Q5PSW7, UniProt: P0AD64*PLUS, beta-lactamase
#2: Chemical ChemComp-SA2 / (3R)-4-[(4-CARBOXYBUTANOYL)OXY]-N-[(1E)-3-OXOPROP-1-EN-1-YL]-3-SULFINO-D-VALINE / 4-AZA-5-CARBOXY-6-SULFENATE-6-METHYL-8-OXA-9-OXO-TRIS-2-TRANS-DECENEDIOIC ACID


Mass: 365.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19NO9S
#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.: 248 / 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: 38.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 21-30% PEG6000, 0.1M HEPES pH6.8-8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
PH range: 6.8-8.2

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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: May 20, 2005
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→46.23 Å / Num. all: 41734 / Num. obs: 41442 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.45→1.5 Å / % possible all: 97.5

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Processing

Software
NameVersionClassification
d*TREKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→33.84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.264 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19713 2092 5.1 %RANDOM
Rwork0.18047 ---
all0.18131 41734 --
obs0.18131 39329 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.581 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.45→33.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 68 248 2338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222231
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3112.0063045
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4665297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7523.36895
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14815393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7391524
X-RAY DIFFRACTIONr_chiral_restr0.0770.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021652
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21129
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21580
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.62121407
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.20432208
X-RAY DIFFRACTIONr_scbond_it2.1342915
X-RAY DIFFRACTIONr_scangle_it3.2253819
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 153 -
Rwork0.371 2805 -
obs--97.11 %

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