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- PDB-2g9d: Crystal Structure of Succinylglutamate desuccinylase from Vibrio ... -

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Basic information

Entry
Database: PDB / ID: 2g9d
TitleCrystal Structure of Succinylglutamate desuccinylase from Vibrio cholerae, Northeast Structural Genomics Target VcR20
ComponentsSuccinylglutamate desuccinylase
KeywordsHYDROLASE / alpha-beta protein / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


succinylglutamate desuccinylase / succinylglutamate desuccinylase activity / arginine catabolic process to succinate / arginine catabolic process to glutamate / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / hydrolase activity, acting on ester bonds / arginine catabolic process / zinc ion binding / cytosol
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #630 / Succinylglutamate desuccinylase / Succinylglutamate desuccinylase/aspartoacylase / Succinylglutamate desuccinylase / Aspartoacylase family / Zn peptidases / Aminopeptidase / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Succinylglutamate desuccinylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsZhou, W. / Jayaraman, S. / Forouhar, F. / Conover, K. / Rong, X. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Succinylglutamate desuccinylase from Vibrio cholerae, Northeast Structural Genomics Target VcR20.
Authors: Zhou, W. / Jayaraman, S. / Forouhar, F. / Conover, K. / Rong, X. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMar 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Succinylglutamate desuccinylase


Theoretical massNumber of molelcules
Total (without water)40,7841
Polymers40,7841
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.934, 82.934, 116.665
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Succinylglutamate desuccinylase


Mass: 40783.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: MO10 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic
References: UniProt: Q9KSL4, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7
Details: 100 mM MOPS, 2880 mM Potassium Acetate, 5 mM DDT, pH 7.0, Microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97929, 0.97944, 0.96794
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.979441
30.967941
ReflectionResolution: 3→23.94 Å / Num. all: 17694 / Num. obs: 17624 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.069 / Rsym value: 0.065 / Net I/σ(I): 24.49
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 6.1 / Rsym value: 0.355 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3→23.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 426177.92 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: XtalView was also used for the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1671 9.6 %RANDOM
Rwork0.241 ---
obs0.241 17351 96.6 %-
all-17624 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.1508 Å2 / ksol: 0.307303 e/Å3
Displacement parametersBiso mean: 63.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å214.35 Å20 Å2
2--1.19 Å20 Å2
3----2.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3→23.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2735 0 0 17 2752
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 267 9.7 %
Rwork0.333 2484 -
obs--90.1 %

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