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- PDB-4fcf: K234R: apo structure of inhibitor resistant beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 4fcf
TitleK234R: apo structure of inhibitor resistant beta-lactamase
ComponentsBeta-lactamase SHV-1
Keywordshydrolase/hydrolase inhibitor / class A beta-lactamse / 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 / 2-AMINOETHANESULFONIC ACID / Beta-lactamase SHV-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous replacement / Resolution: 1.09 Å
AuthorsRodkey, E.A. / van den Akker, F.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Design and exploration of novel boronic acid inhibitors reveals important interactions with a clavulanic acid-resistant sulfhydryl-variable (SHV) beta-lactamase.
Authors: Winkler, M.L. / Rodkey, E.A. / Taracila, M.A. / Drawz, S.M. / Bethel, C.R. / Papp-Wallace, K.M. / Smith, K.M. / Xu, Y. / Dwulit-Smith, J.R. / Romagnoli, C. / Caselli, E. / Prati, F. / van ...Authors: Winkler, M.L. / Rodkey, E.A. / Taracila, M.A. / Drawz, S.M. / Bethel, C.R. / Papp-Wallace, K.M. / Smith, K.M. / Xu, Y. / Dwulit-Smith, J.R. / Romagnoli, C. / Caselli, E. / Prati, F. / van den Akker, F. / Bonomo, R.A.
History
DepositionMay 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references

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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)30,0774
Polymers28,9351
Non-polymers1,1423
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.631, 55.416, 83.951
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: 28935.033 Da / Num. of mol.: 1 / Fragment: unp residues 22-286 / Mutation: K234R
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-TAU / 2-AMINOETHANESULFONIC ACID / Taurine


Mass: 125.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7NO3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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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: 296 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 21-30% PEG6K, 0.1M Hepes pH 6.6-7.6, 0.56mM cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 2, 2012
RadiationMonochromator: Double crystal monochromator, Rh coated flat mirror, toroidal focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.09→50 Å / Num. all: 100011 / Num. obs: 84309 / % possible obs: 84.3 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.08→1.12 Å / % possible all: 82.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.6.0117phasing
RefinementMethod to determine structure: isomorphous replacement / Resolution: 1.09→23.8 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.624 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14961 4165 5 %RANDOM
Rwork0.12293 ---
obs0.12424 79974 84.83 %-
all-94309 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.727 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.09→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 49 229 2304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222311
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.671.9953157
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0825306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16922.82899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57115401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7831528
X-RAY DIFFRACTIONr_chiral_restr0.1130.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211756
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_it1.6241.51447
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.32522343
X-RAY DIFFRACTIONr_scbond_it3.2363864
X-RAY DIFFRACTIONr_scangle_it4.5964.5813
X-RAY DIFFRACTIONr_rigid_bond_restr1.62432311
X-RAY DIFFRACTIONr_sphericity_free10.7393229
X-RAY DIFFRACTIONr_sphericity_bonded6.34832259
LS refinement shellResolution: 1.082→1.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.143 349 -
Rwork0.113 6074 -
obs--88.67 %

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