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- PDB-3d4f: SHV-1 beta-lactamase complex with LN1-255 -

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Basic information

Entry
Database: PDB / ID: 3d4f
TitleSHV-1 beta-lactamase complex with LN1-255
ComponentsBeta-lactamase SHV-1
KeywordsHYDROLASE / BETA-LACTAMASE INHIBITOR / DRUG DESIGN / Antibiotic resistance / Plasmid
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-LN1 / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE / Beta-lactamase SHV-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPattanaik, P. / Bethel, C.R. / Hujer, A.M. / Bonomo, R.A. / Buynak, J.D. / van den Akker, F.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Strategic Design of an Effective {beta}-Lactamase Inhibitor: LN-1-255, A 6-ALKYLIDENE-2'-SUBSTITUTED PENICILLIN SULFONE
Authors: Pattanaik, P. / Bethel, C.R. / Hujer, A.M. / Hujer, K.M. / Distler, A.M. / Taracila, M. / Anderson, V.E. / Fritsche, T.R. / Jones, R.N. / Pagadala, S.R. / van den Akker, F. / Buynak, J.D. / Bonomo, R.A.
History
DepositionMay 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: 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 1.3Oct 9, 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)32,7684
Polymers31,2601
Non-polymers1,5083
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)49.611, 55.503, 83.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMonomer

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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 / Plasmid: PBC SK(-) / Production host: Escherichia coli (E. coli) / Strain (production host): DH10B / 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-LN1 / (3R)-4-{[(3,4-dihydroxyphenyl)acetyl]oxy}-N-(2-formylindolizin-3-yl)-3-sulfino-D-valine


Mass: 490.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N2O9S
#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: 1.84 Å3/Da / Density % sol: 33.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30% PEG6000, 0.1M HEPES pH7. 0.56mM Cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2006
RadiationMonochromator: vertically focusing mirror and a horizontally focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 34280 / Num. obs: 33525 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.8 Å2 / Rsym value: 0.101 / Net I/σ(I): 20.8
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.1 / % possible all: 96.3

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SHV-1 wt

Resolution: 1.55→31.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1336274.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1659 5 %RANDOM
Rwork0.168 ---
obs0.168 33435 97.7 %-
all-34222 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.5903 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 17 Å2
Baniso -1Baniso -2Baniso -3
1-3.29 Å20 Å20 Å2
2---4.05 Å20 Å2
3---0.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.55→31.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 101 248 2373
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.08
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 278 5.1 %
Rwork0.247 5188 -
obs-3876 97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ln1-24hrs_d5.parnew_ligands_24hr_9.top
X-RAY DIFFRACTION4new_cymal.par
X-RAY DIFFRACTION5cis167new.par

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