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- PDB-5ee8: Crystal structure of S02030 boronic acid inhibitor complexed to S... -

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Basic information

Entry
Database: PDB / ID: 5ee8
TitleCrystal structure of S02030 boronic acid inhibitor complexed to SHV-1 beta-lactamase
ComponentsBeta-lactamase SHV-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / transition state inhibitor / 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-ZXM / Beta-lactamase SHV-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsKrishnan, N. / van den Akker, F.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2016
Title: Crystal Structures of KPC-2 and SHV-1 beta-Lactamases in Complex with the Boronic Acid Transition State Analog S02030.
Authors: Nguyen, N.Q. / Krishnan, N.P. / Rojas, L.J. / Prati, F. / Caselli, E. / Romagnoli, C. / Bonomo, R.A. / van den Akker, F.
History
DepositionOct 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 23, 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)30,2484
Polymers28,9071
Non-polymers1,3413
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.567, 55.185, 83.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
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-ZXM / 1-{(2R)-2-(dihydroxyboranyl)-2-[(thiophen-2-ylacetyl)amino]ethyl}-1H-1,2,3-triazole-4-carboxylic acid


Mass: 324.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13BN4O5S
#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.: 217 / 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: 1.98 Å3/Da / Density % sol: 37.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20-30% PEG 6000, 100mM Tris pH 7.5, 0.56mM cymal-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 11, 2014
RadiationMonochromator: 1.1271 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 33737 / % possible obs: 97 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.039 / Rrim(I) all: 0.081 / Χ2: 1.051 / Net I/av σ(I): 16.548 / Net I/σ(I): 10.7 / Num. measured all: 122260
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.54-1.63.50.4233650.8120.2460.4921.09498.3
1.6-1.663.60.32833750.840.190.3831.08898.6
1.66-1.733.60.27133830.910.1570.3161.07498.7
1.73-1.833.60.21133710.9480.1190.2441.05298.5
1.83-1.943.60.15733840.9690.0870.1821.07298.2
1.94-2.093.60.11833740.9780.0640.1351.00497.6
2.09-2.33.70.09433700.9890.050.1071.01897.4
2.3-2.633.70.07833730.9920.0420.0891.06796.2
2.63-3.323.70.05933520.9950.0320.0671.02995.1
3.32-503.70.02733900.9990.0150.0311.01791.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H5S

2h5s


Resolution: 1.54→33.3 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.354 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1753 1686 5 %RANDOM
Rwork0.1493 ---
obs0.1506 32017 96.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.42 Å2 / Biso mean: 15.141 Å2 / Biso min: 8.15 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.54→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 97 217 2338
Biso mean--20.79 28.82 -
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192270
X-RAY DIFFRACTIONr_bond_other_d0.0010.022215
X-RAY DIFFRACTIONr_angle_refined_deg1.7092.0183091
X-RAY DIFFRACTIONr_angle_other_deg0.9435103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50923.02196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00415386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4091526
X-RAY DIFFRACTIONr_chiral_restr0.0920.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212558
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02507
X-RAY DIFFRACTIONr_mcbond_it1.0211.2751115
X-RAY DIFFRACTIONr_mcbond_other1.0211.2741114
X-RAY DIFFRACTIONr_mcangle_it1.5691.911409
LS refinement shellResolution: 1.538→1.578 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 115 -
Rwork0.215 2332 -
all-2447 -
obs--96.8 %

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