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- PDB-1vgy: Crystal structure of succinyl diaminopimelate desuccinylase -

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Basic information

Entry
Database: PDB / ID: 1vgy
TitleCrystal structure of succinyl diaminopimelate desuccinylase
Componentssuccinyl-diaminopimelate desuccinylase
KeywordsStructural genomics / unknown function
Function / homology
Function and homology information


acetylornithine deacetylase activity / succinyl-diaminopimelate desuccinylase activity / succinyl-diaminopimelate desuccinylase / L-arginine biosynthetic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cobalt ion binding / zinc ion binding
Similarity search - Function
Succinyl-diaminopimelate desuccinylase, proteobacteria / : / Alpha-Beta Plaits - #360 / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase ...Succinyl-diaminopimelate desuccinylase, proteobacteria / : / Alpha-Beta Plaits - #360 / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Succinyl-diaminopimelate desuccinylase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-Met SAD phasing / Resolution: 1.9 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionNov 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: succinyl-diaminopimelate desuccinylase
B: succinyl-diaminopimelate desuccinylase


Theoretical massNumber of molelcules
Total (without water)86,1912
Polymers86,1912
Non-polymers00
Water13,547752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.655, 56.500, 101.400
Angle α, β, γ (deg.)90.00, 103.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein succinyl-diaminopimelate desuccinylase


Mass: 43095.562 Da / Num. of mol.: 2 / Mutation: L30(MSE), L44(MSE), I335(MSE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: dapE / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JYL2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 752 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.79→39.84 Å / Num. all: 81454 / Num. obs: 81454 / % possible obs: 97.6 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.6
Reflection shellResolution: 1.79→1.89 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.02167 / Mean I/σ(I) obs: 0.9 / % possible all: 84
Reflection shell
*PLUS
% possible obs: 84 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMAC4refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: Se-Met SAD phasing / Resolution: 1.9→39.84 Å / σ(F): 0
RfactorNum. reflection
Rfree0.266 3597
Rwork0.213 -
obs-71896
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 316.381 Å2 / ksol: 0.927 e/Å3
Displacement parametersBiso mean: 33.477 Å2
Baniso -1Baniso -2Baniso -3
1-0.059 Å20 Å2-0.23 Å2
2--0.499 Å20 Å2
3----0.662 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 1.9→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5706 0 0 752 6458
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d2.364
X-RAY DIFFRACTIONp_planar_tor2.519
X-RAY DIFFRACTIONp_chiral_restr0.152
X-RAY DIFFRACTIONp_plane_restr0.013
X-RAY DIFFRACTIONp_mcbond_it1.711
X-RAY DIFFRACTIONp_mcangle_it2.696
X-RAY DIFFRACTIONp_scbond_it3.047
X-RAY DIFFRACTIONp_scangle_it4.268
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.4

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