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- PDB-5gtd: o-Succinylbenzoate CoA Synthetase (MenE) from Bacillus Subtilis i... -

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Basic information

Entry
Database: PDB / ID: 5gtd
Titleo-Succinylbenzoate CoA Synthetase (MenE) from Bacillus Subtilis in Complex with the Acyl-adenylate Intermediate OSB-AMP
Components2-succinylbenzoate--CoA ligase
KeywordsLIGASE / Adenylate-forming Enzyme / adenylate intermdiate / OSBAMP / in-line backside nucleophilic substitution / strained conformation
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 ...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 / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / IMIDAZOLE / 2-SUCCINYLBENZOATE / DI(HYDROXYETHYL)ETHER / 2-succinylbenzoate--CoA ligase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsChen, Y. / Guo, Z.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
the University Grants Council of the Government of the Hong Kong Special Administrative RegionSBI14SC05 Hong Kong
Citation
Journal: Biochemistry / Year: 2016
Title: Mechanistic Insights from the Crystal Structure of Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase Complexed with the Adenylate Intermediate
Authors: Chen, Y. / Jiang, Y. / Guo, Z.
#1: Journal: 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
DepositionAug 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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 / struct_conn_type
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_type.id
Revision 2.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_site.pdbx_auth_comp_id

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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)112,01813
Polymers110,5382
Non-polymers1,48011
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-46 kcal/mol
Surface area32970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.814, 121.814, 98.563
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 2 molecules AB

#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 (E. coli) / References: UniProt: P23971, o-succinylbenzoate-CoA ligase

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Non-polymers , 7 types, 50 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-OSB / 2-SUCCINYLBENZOATE / O-SUCCINYLBENZOATE


Mass: 222.194 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10O5
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.31 Å3/Da / Density % sol: 62.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 10% PEG 6000, 10.5% MPD, 0.094M HEPES pH7.3, 0.012M imidazole, 0.12M sodium acetate, 0.6% PEG8000, 0.48% ethylene glycol
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.69→31.96 Å / Num. obs: 39783 / % possible obs: 99.17 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.083 / Rsym value: 0.089 / Net I/σ(I): 19.4
Reflection shellResolution: 2.69→2.79 Å / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 3.2 / CC1/2: 0.868 / % possible all: 98.75

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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: 5BUR

5bur


Resolution: 2.69→31.96 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 1996 5.02 %
Rwork0.1997 --
obs0.2015 39781 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.69→31.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6355 0 93 39 6487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036582
X-RAY DIFFRACTIONf_angle_d0.7198966
X-RAY DIFFRACTIONf_dihedral_angle_d12.6432255
X-RAY DIFFRACTIONf_chiral_restr0.0251039
X-RAY DIFFRACTIONf_plane_restr0.0021153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6904-2.75770.33541400.28372699X-RAY DIFFRACTION98
2.7577-2.83220.31561440.27072693X-RAY DIFFRACTION100
2.8322-2.91550.33641440.25522661X-RAY DIFFRACTION100
2.9155-3.00950.30931440.2592735X-RAY DIFFRACTION100
3.0095-3.1170.31291410.252682X-RAY DIFFRACTION100
3.117-3.24170.29881410.22952687X-RAY DIFFRACTION100
3.2417-3.3890.241420.23522712X-RAY DIFFRACTION99
3.389-3.56750.28391420.24362686X-RAY DIFFRACTION99
3.5675-3.79070.26081430.23152661X-RAY DIFFRACTION97
3.7907-4.08280.24221410.18532684X-RAY DIFFRACTION99
4.0828-4.49270.20931430.16942723X-RAY DIFFRACTION100
4.4927-5.14050.20221440.17082718X-RAY DIFFRACTION100
5.1405-6.46760.23621420.19582754X-RAY DIFFRACTION100
6.4676-31.96190.19281450.16822690X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 51.9746 Å / Origin y: -143.5064 Å / Origin z: 0.978 Å
111213212223313233
T0.6499 Å20.0075 Å2-0.1465 Å2-0.4271 Å20.0044 Å2--0.5558 Å2
L1.0617 °2-0.2095 °2-0.4138 °2-3.8223 °21.3217 °2--1.9991 °2
S-0.0374 Å °-0.0891 Å °-0.1177 Å °-0.0813 Å °-0.4086 Å °0.3582 Å °-0.3654 Å °-0.1474 Å °0.3548 Å °
Refinement TLS groupSelection details: all

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