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- PDB-3ipl: CRYSTAL STRUCTURE OF o-succinylbenzoic acid-CoA ligase FROM Staph... -

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Basic information

Entry
Database: PDB / ID: 3ipl
TitleCRYSTAL STRUCTURE OF o-succinylbenzoic acid-CoA ligase FROM Staphylococcus aureus subsp. aureus Mu50
Components2-succinylbenzoate--CoA ligase
KeywordsLIGASE / STRUCTURAL GENOMICS / acyl-protein synthetase / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC / ATP-binding / Menaquinone biosynthesis / Nucleotide-binding
Function / homology
Function and homology information


o-succinylbenzoate-CoA ligase / o-succinylbenzoate-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 / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / Rossmann fold ...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 / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-succinylbenzoate--CoA ligase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsPatskovsky, Y. / Toro, R. / Dickey, M. / Chang, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of o-succinylbenzoic acid-CoA ligase from Staphylococcus aureus
Authors: Patskovsky, Y. / Toro, R. / Dickey, M. / Sauder, J.M. / Chang, S. / Burley, S.K. / Almo, S.C.
History
DepositionAug 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 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
B: 2-succinylbenzoate--CoA ligase
C: 2-succinylbenzoate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)169,7073
Polymers169,7073
Non-polymers00
Water7,512417
1
A: 2-succinylbenzoate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)56,5691
Polymers56,5691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-succinylbenzoate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)56,5691
Polymers56,5691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 2-succinylbenzoate--CoA ligase


Theoretical massNumber of molelcules
Total (without water)56,5691
Polymers56,5691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)199.509, 65.425, 114.956
Angle α, β, γ (deg.)90.00, 100.05, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
/ NCS ensembles :
ID
1
2

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Components

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


Mass: 56569.117 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria)
Gene: LuxE, menE, SA1615 / Plasmid: MODIFIED PET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63526, o-succinylbenzoate-CoA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M BIS-TRIS, PH 5.5, 200MM LITHIUM SULFATE, 25% PEG3350, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 65021 / % possible obs: 99.6 % / Observed criterion σ(I): -5 / Redundancy: 1.9 % / Biso Wilson estimate: 42.383 Å2 / Rsym value: 0.113 / Net I/σ(I): 4.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 0.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SHELXmodel building
RESOLVEmodel building
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.711 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24146 1309 2 %RANDOM
Rwork0.18456 ---
obs0.18575 63082 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.729 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å21.22 Å2
2--2.55 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10061 0 0 417 10478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210309
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.95414046
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55751308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57225.041484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.183151802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4721543
X-RAY DIFFRACTIONr_chiral_restr0.0930.21590
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027821
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1440.34537
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.56987
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.5771
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1160.390
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.528
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.30526513
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.051310275
X-RAY DIFFRACTIONr_scbond_it5.63334331
X-RAY DIFFRACTIONr_scangle_it8.00653739
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
12617medium positional0.570.5
12617medium positional0.560
12617medium positional0.460
2590medium positional0.410.5
12617medium thermal6.215
12617medium thermal6.260
12617medium thermal4.960
2590medium thermal18.015
LS refinement shellResolution: 2.3→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 85 -
Rwork0.274 4285 -
obs--92.55 %

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