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- PDB-6nj0: Wild-type E. coli MenE with bound m phenylether-linked analogue o... -

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Basic information

Entry
Database: PDB / ID: 6nj0
TitleWild-type E. coli MenE with bound m phenylether-linked analogue of OSB-AMS
Components2-succinylbenzoate--CoA ligase
KeywordsLIGASE / MenE / E. coli / menaquinone
Function / homology
Function and homology information


o-succinylbenzoate-CoA ligase / o-succinylbenzoate-CoA ligase activity / menaquinone biosynthetic process / protein-containing complex / ATP binding / identical protein binding
Similarity search - Function
2-succinylbenzoate--CoA ligase / : / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Chem-KOY / 2-succinylbenzoate--CoA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.83 Å
AuthorsSi, Y. / Yin, Y. / French, J.B. / Tonge, P.J.
CitationJournal: Biochemistry / Year: 2019
Title: Structure-Based Design, Synthesis, and Biological Evaluation of Non-Acyl Sulfamate Inhibitors of the Adenylate-Forming Enzyme MenE.
Authors: Evans, C.E. / Si, Y. / Matarlo, J.S. / Yin, Y. / French, J.B. / Tonge, P.J. / Tan, D.S.
History
DepositionJan 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-succinylbenzoate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7562
Polymers50,2361
Non-polymers5201
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.146, 74.424, 79.033
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 2-succinylbenzoate--CoA ligase / o-succinylbenzoyl-CoA synthetase / OSB-CoA synthetase


Mass: 50236.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: menE, b2260, JW2255 / Production host: Escherichia coli (E. coli) / References: UniProt: P37353, o-succinylbenzoate-CoA ligase
#2: Chemical ChemComp-KOY / 5'-O-{3-[3-(2-carboxyphenyl)-3-oxopropyl]phenyl}adenosine


Mass: 519.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25N5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, magnesium chloride, tris hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.918061 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918061 Å / Relative weight: 1
ReflectionResolution: 1.83→54.18 Å / Num. obs: 37301 / % possible obs: 99.3 % / Redundancy: 10 % / CC1/2: 0.994 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.068 / Rrim(I) all: 0.158 / Net I/σ(I): 10.3
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.631 / Num. unique obs: 2473 / CC1/2: 0.814 / Rpim(I) all: 0.304 / Rrim(I) all: 0.703 / % possible all: 90.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 1.83→54.18 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.865 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24434 1803 4.8 %RANDOM
Rwork0.19617 ---
obs0.19854 35441 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.808 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.83→54.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 38 258 3580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193421
X-RAY DIFFRACTIONr_bond_other_d0.0030.023120
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.964660
X-RAY DIFFRACTIONr_angle_other_deg1.0833.0037165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9585436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4622.713129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27715506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3551524
X-RAY DIFFRACTIONr_chiral_restr0.1250.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213827
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02724
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_it2.3782.6931751
X-RAY DIFFRACTIONr_mcbond_other2.3772.6931750
X-RAY DIFFRACTIONr_mcangle_it3.2464.0232181
X-RAY DIFFRACTIONr_mcangle_other3.2464.0242182
X-RAY DIFFRACTIONr_scbond_it2.7532.8511670
X-RAY DIFFRACTIONr_scbond_other2.7512.8511668
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8644.1832478
X-RAY DIFFRACTIONr_long_range_B_refined5.14131.4223834
X-RAY DIFFRACTIONr_long_range_B_other5.1431.4193835
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.833→1.881 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 112 -
Rwork0.295 2384 -
obs--91.73 %

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