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- PDB-4x69: Crystal structure of OP0595 complexed with CTX-M-44 -

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Basic information

Entry
Database: PDB / ID: 4x69
TitleCrystal structure of OP0595 complexed with CTX-M-44
ComponentsBeta-lactamase Toho-1
KeywordsHYDROLASE/HYDROLASE 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
Chem-OP0 / Beta-lactamase Toho-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsYamada, M. / Watanabe, T.
CitationJournal: J.Antimicrob.Chemother. / Year: 2015
Title: OP0595, a new diazabicyclooctane: mode of action as a serine beta-lactamase inhibitor, antibiotic and beta-lactam 'enhancer'
Authors: Morinaka, A. / Tsutsumi, Y. / Yamada, M. / Suzuki, K. / Watanabe, T. / Abe, T. / Furuuchi, T. / Inamura, S. / Sakamaki, Y. / Mitsuhashi, N. / Ida, T. / Livermore, D.M.
History
DepositionDec 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Derived calculations
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase Toho-1
B: Beta-lactamase Toho-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2736
Polymers56,4962
Non-polymers7774
Water6,630368
1
A: Beta-lactamase Toho-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6363
Polymers28,2481
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint3 kcal/mol
Surface area10850 Å2
MethodPISA
2
B: Beta-lactamase Toho-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6363
Polymers28,2481
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint3 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.533, 72.982, 63.052
Angle α, β, γ (deg.)90.000, 109.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase Toho-1


Mass: 28247.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q47066, beta-lactamase
#2: Chemical ChemComp-OP0 / (2S,5R)-N-(2-aminoethoxy)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide


Mass: 326.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18N4O7S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 37.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: PEG 6000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 21, 2013
Diffraction measurementDetails: 0.50 degrees, 4.0 sec, detector distance 129.80 mm / Method: \w scans
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.07 / Number: 291155
ReflectionResolution: 1.42→50 Å / Num. obs: 81658 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 24.195
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.173 / Rsym value: 0.455 / % possible all: 80.5
Cell measurementReflection used: 291155

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IYS

1iys


Resolution: 1.42→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / Matrix type: sparse / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.177 / SU B: 1.049 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 4113 5 %RANDOM
Rwork0.1835 77420 --
obs0.1848 77420 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 38.37 Å2 / Biso mean: 12.367 Å2 / Biso min: 5.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20.1 Å2
2---0.37 Å20 Å2
3---0.69 Å2
Refinement stepCycle: final / Resolution: 1.42→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 48 368 4368
Biso mean--11.91 22.03 -
Num. residues----522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224086
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.9745551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0175526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37924.675169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44215695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4451527
X-RAY DIFFRACTIONr_chiral_restr0.0840.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213047
X-RAY DIFFRACTIONr_mcbond_it0.5751.52618
X-RAY DIFFRACTIONr_mcangle_it1.05324199
X-RAY DIFFRACTIONr_scbond_it1.78931468
X-RAY DIFFRACTIONr_scangle_it3.0184.51352
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.42-1.4570.2992640.2814786611082.6510.25
1.457-1.4970.252980.2475247594193.3340.212
1.497-1.540.2272960.2165518584099.5550.183
1.54-1.5870.2333060.2035295560499.9460.17
1.587-1.6390.2162810.1825178546099.9820.152
1.639-1.6970.2212760.182500952851000.153
1.697-1.7610.212570.174484951061000.148
1.761-1.8330.22340.175465248861000.15
1.833-1.9140.1932270.1714543477199.9790.151
1.914-2.0070.1692110.166423944501000.15
2.007-2.1160.2021960.173410443001000.161
2.116-2.2440.1871790.171390340821000.162
2.244-2.3980.1941880.1743602379299.9470.166
2.398-2.590.1891780.1723397357699.9720.168
2.59-2.8370.2121790.177309832771000.179
2.837-3.170.1991520.1862819297299.9660.191
3.17-3.6580.211230.1752494261899.9620.189
3.658-4.4740.211230.1662116224099.9550.188
4.474-6.3020.23990.1991642174299.9430.234
6.302-500.218460.23192999298.2860.272

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