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- PDB-4x68: Crystal Structure of OP0595 complexed with AmpC -

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Basic information

Entry
Database: PDB / ID: 4x68
TitleCrystal Structure of OP0595 complexed with AmpC
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Chem-OP0 / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 1.1Oct 14, 2015Group: Database references
Revision 1.2Feb 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 1.3Nov 8, 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 / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,2956
Polymers78,5252
Non-polymers7704
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-18 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.027, 54.781, 75.667
Angle α, β, γ (deg.)90.000, 90.800, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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Components

#1: Protein Beta-lactamase / / Cephalosporinase


Mass: 39262.348 Da / Num. of mol.: 2 / Fragment: UNP residues 32-387
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: ampC, PA4110 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P24735, 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-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 1.95 Å3/Da / Density % sol: 37.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: PEG 2000 monomethylether, NiCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 9, 2012
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 67982 / % possible obs: 98.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.074 / Χ2: 2.343 / Net I/av σ(I): 27.056 / Net I/σ(I): 10.8 / Num. measured all: 246153
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.68-1.7430.56463481.29292.5
1.74-1.813.40.44566421.34296.9
1.81-1.893.60.33567361.43797.6
1.89-1.993.60.22967571.52698.2
1.99-2.123.70.16268361.72999
2.12-2.283.70.12468441.99399.5
2.28-2.513.80.10468782.39599.7
2.51-2.873.80.09869363.65999.9
2.87-3.623.80.06969434.094100
3.62-503.70.0470623.20199.5

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Processing

Software
NameVersionClassification
REFMACrefmac_5.5.0109refinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WZX

2wzx


Resolution: 1.68→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.801 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 3308 4.9 %RANDOM
Rwork0.2117 64640 --
obs0.2134 67948 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.31 Å2 / Biso mean: 22.89 Å2 / Biso min: 11.18 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å2-0.24 Å2
2---1.53 Å20 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 1.68→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5546 0 44 242 5832
Biso mean--34.19 26.94 -
Num. residues----714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225728
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.9827792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7725712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70523.333264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7615894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3681548
X-RAY DIFFRACTIONr_chiral_restr0.0760.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214480
X-RAY DIFFRACTIONr_mcbond_it0.5451.53562
X-RAY DIFFRACTIONr_mcangle_it1.01325672
X-RAY DIFFRACTIONr_scbond_it1.52532166
X-RAY DIFFRACTIONr_scangle_it2.5694.52120
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 211 -
Rwork0.319 4308 -
all-4519 -
obs--88.56 %

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