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- PDB-5c5h: R195K E. coli MenE with bound OSB-AMS -

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Basic information

Entry
Database: PDB / ID: 5c5h
TitleR195K E. coli MenE with bound OSB-AMS
Components2-succinylbenzoate--CoA ligase
KeywordsLIGASE
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, C-terminal domain superfamily / AMP-binding enzyme
Similarity search - Domain/homology
Chem-4YB / 2-succinylbenzoate--CoA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsMatarlo, J.S. / Shek, R. / Rajashankar, K.R. / Tonge, P.J. / French, J.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102864 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
CitationJournal: Biochemistry / Year: 2015
Title: Mechanism of MenE Inhibition by Acyl-Adenylate Analogues and Discovery of Novel Antibacterial Agents.
Authors: Matarlo, J.S. / Evans, C.E. / Sharma, I. / Lavaud, L.J. / Ngo, S.C. / Shek, R. / Rajashankar, K.R. / French, J.B. / Tan, D.S. / Tonge, P.J.
History
DepositionJun 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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.pdbx_dist_value / _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_symmetry

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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)102,0417
Polymers100,8672
Non-polymers1,1745
Water4,017223
1
A: 2-succinylbenzoate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0083
Polymers50,4341
Non-polymers5752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-succinylbenzoate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0334
Polymers50,4341
Non-polymers5993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.060, 126.060, 111.752
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

21B-660-

HOH

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Components

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


Mass: 50433.664 Da / Num. of mol.: 2 / Mutation: R195K
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-4YB / 5'-O-{[4-(2-carboxyphenyl)-4-oxobutanoyl]sulfamoyl}adenosine


Mass: 550.499 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H22N6O10S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 18-22% Peg 4,000 0.2 M MgCl2 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.078 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 38130 / % possible obs: 99.9 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 20.3
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.924 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IPL and 1T5D

3ipl

1t5d


Resolution: 2.401→41.26 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.907 / SU B: 7.965 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.427 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24717 2015 5 %RANDOM
Rwork0.20019 ---
obs0.2026 38130 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.891 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å20 Å2
2--0.15 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.401→41.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6854 0 79 224 7157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197125
X-RAY DIFFRACTIONr_bond_other_d0.0020.026742
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.969740
X-RAY DIFFRACTIONr_angle_other_deg0.7453.00315405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1845888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63123.7300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.576151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4621547
X-RAY DIFFRACTIONr_chiral_restr0.0630.21097
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021665
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_it1.5373.923561
X-RAY DIFFRACTIONr_mcbond_other1.5373.9193560
X-RAY DIFFRACTIONr_mcangle_it2.585.8674440
X-RAY DIFFRACTIONr_mcangle_other2.5795.8684441
X-RAY DIFFRACTIONr_scbond_it1.4453.9893564
X-RAY DIFFRACTIONr_scbond_other1.4453.9893565
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4735.9245299
X-RAY DIFFRACTIONr_long_range_B_refined4.32330.2777814
X-RAY DIFFRACTIONr_long_range_B_other4.32330.2767815
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 135 -
Rwork0.267 2700 -
obs--96.99 %

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