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- PDB-5bus: O-succinylbenzoate Coenzyme A Synthetase (MenE) from Bacillus Sub... -

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Basic information

Entry
Database: PDB / ID: 5bus
TitleO-succinylbenzoate Coenzyme A Synthetase (MenE) from Bacillus Subtilis, in complex with AMP
Components2-succinylbenzoate--CoA ligase
KeywordsLIGASE / AMP / enzyme mechanism / protein conformation / vitamin K2 / adenylate forming enzyme / domain alteration / open-closed conformational change
Function / homology
Function and homology information


o-succinylbenzoate-CoA ligase / o-succinylbenzoate-CoA ligase activity / CoA-ligase activity / menaquinone biosynthetic process / ATP binding
Similarity search - Function
2-succinylbenzoate--CoA ligase / ANL, C-terminal domain / ANL, N-terminal domain / 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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase ...2-succinylbenzoate--CoA ligase / ANL, C-terminal domain / ANL, N-terminal domain / 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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 2-succinylbenzoate--CoA ligase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsChen, Y. / Sun, Y. / Song, H. / Guo, Z.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
HKSAR GovernmentGRF601413 Hong Kong
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for the ATP-dependent Configuration of Adenylation Active Site in Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase
Authors: Chen, Y. / Sun, Y. / Song, H. / Guo, Z.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Nov 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)111,3748
Polymers110,5382
Non-polymers8366
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-45 kcal/mol
Surface area33640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.811, 121.811, 98.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein 2-succinylbenzoate--CoA ligase / o-succinylbenzoyl-CoA synthetase / OSB-CoA synthetase


Mass: 55269.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: menE, BSU30790 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P23971, o-succinylbenzoate-CoA ligase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH7.5, 10% (w/v) PEG6000, 5% (v/v) MPD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.973 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2014
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.603→38.52 Å / Num. obs: 43794 / % possible obs: 99.46 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.136 / Rsym value: 0.15 / Net I/σ(I): 6.6
Reflection shellResolution: 2.603→2.696 Å / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 4.93 / % possible all: 99.34

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BUQ

5buq


Resolution: 2.603→38.52 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2335 1997 4.56 %
Rwork0.1904 --
obs0.1924 43772 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.603→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6352 0 50 62 6464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086571
X-RAY DIFFRACTIONf_angle_d1.1688948
X-RAY DIFFRACTIONf_dihedral_angle_d13.52258
X-RAY DIFFRACTIONf_chiral_restr0.0451038
X-RAY DIFFRACTIONf_plane_restr0.0051150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6031-2.66820.31761400.23332937X-RAY DIFFRACTION100
2.6682-2.74030.24141490.21932992X-RAY DIFFRACTION100
2.7403-2.8210.30211410.22262978X-RAY DIFFRACTION100
2.821-2.9120.29091450.22083000X-RAY DIFFRACTION100
2.912-3.0160.27771400.22632966X-RAY DIFFRACTION100
3.016-3.13670.28041460.21992996X-RAY DIFFRACTION100
3.1367-3.27940.29491370.2122992X-RAY DIFFRACTION100
3.2794-3.45220.25681420.20883004X-RAY DIFFRACTION100
3.4522-3.66830.28281450.19713001X-RAY DIFFRACTION100
3.6683-3.95130.20931430.17832988X-RAY DIFFRACTION100
3.9513-4.34850.22821430.172996X-RAY DIFFRACTION100
4.3485-4.97660.17811470.16733000X-RAY DIFFRACTION100
4.9766-6.26560.22981380.18733035X-RAY DIFFRACTION100
6.2656-38.52420.20011410.18092890X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 143.1592 Å / Origin y: -51.6171 Å / Origin z: -1.3844 Å
111213212223313233
T0.2537 Å20.0144 Å2-0.0274 Å2-0.3656 Å2-0.0758 Å2--0.3255 Å2
L1.8028 °20.0049 °20.6498 °2-0.3494 °2-0.1389 °2--0.9923 °2
S-0.325 Å °-0.0885 Å °0.2004 Å °-0.0589 Å °0.013 Å °-0.1016 Å °-0.0941 Å °-0.1586 Å °-0.1699 Å °
Refinement TLS groupSelection details: all

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