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- PDB-4r3b: Crystal structure of SHV-1 b-lactamase in complex with 6b-(hydrox... -

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Basic information

Entry
Database: PDB / ID: 4r3b
TitleCrystal structure of SHV-1 b-lactamase in complex with 6b-(hydroxymethyl)penicillanic acid sulfone PSR-283A
ComponentsBeta-lactamase SHV-1
KeywordsHYDROLASE / Class A beta-lactamase / Inactivate b-lactam antibiotics
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
Chem-3GE / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE / Beta-lactamase SHV-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.366 Å
AuthorsRodkey, E.A. / van den Akker, F.
CitationJournal: Biochemistry / Year: 2015
Title: Detecting a Quasi-stable Imine Species on the Reaction Pathway of SHV-1 beta-Lactamase and 6 beta-(Hydroxymethyl)penicillanic Acid Sulfone.
Authors: Che, T. / Rodkey, E.A. / Bethel, C.R. / Shanmugam, S. / Ding, Z. / Pusztai-Carey, M. / Nottingham, M. / Chai, W. / Buynak, J.D. / Bonomo, R.A. / van den Akker, F. / Carey, P.R.
History
DepositionAug 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 2.0May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_conn / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 2.1Oct 16, 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)30,1904
Polymers28,9071
Non-polymers1,2823
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.238, 55.274, 84.465
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: 28907.018 Da / Num. of mol.: 1 / Fragment: SHV-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-3GE / N-[(1E)-2-formyl-3-hydroxyprop-1-en-1-yl]-3-[(S)-sulfino]-D-valine


Mass: 265.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 38.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 21-30% PEG6000, 0.1M HEPES pH 6.2-8.2, 0.56mM Cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
PH range: 6.8-8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 26, 2010
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.366→50 Å / Num. all: 46988 / Num. obs: 46331 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.035 / Net I/σ(I): 28.3
Reflection shellResolution: 1.366→1.42 Å / % possible all: 94.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.366→27.73 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.647 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17213 2470 5.1 %RANDOM
Rwork0.13032 ---
obs0.13242 46331 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.951 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.366→27.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 61 269 2354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222202
X-RAY DIFFRACTIONr_angle_refined_deg1.3592.0042986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.945266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73523.09397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43115394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.161526
X-RAY DIFFRACTIONr_chiral_restr0.0890.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211596
X-RAY DIFFRACTIONr_mcbond_it4.4681.51344
X-RAY DIFFRACTIONr_mcangle_it5.62422176
X-RAY DIFFRACTIONr_scbond_it9.8643858
X-RAY DIFFRACTIONr_scangle_it12.5574.5810
X-RAY DIFFRACTIONr_rigid_bond_restr5.89632202
X-RAY DIFFRACTIONr_sphericity_free22.0223269
X-RAY DIFFRACTIONr_sphericity_bonded11.36632168
LS refinement shellResolution: 1.366→1.402 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 174 -
Rwork0.254 3119 -
obs--91.93 %

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