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- PDB-1yw4: Crystal Structure of the Succinylglutamate Desuccinylase from Chr... -

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Basic information

Entry
Database: PDB / ID: 1yw4
TitleCrystal Structure of the Succinylglutamate Desuccinylase from Chromobacterium violaceum, Northeast Structural Genomics Target CvR22.
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 ester bonds / zinc ion binding
Similarity search - Function
Succinylglutamate desuccinylase / Succinylglutamate desuccinylase/aspartoacylase / Succinylglutamate desuccinylase / Aspartoacylase family / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Succinylglutamate desuccinylase
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsForouhar, F. / Abashidze, M. / Conover, K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Succinylglutamate Desuccinylase from Chromobacterium violaceum, Northeast Structural Genomics Target CvR22.
Authors: Forouhar, F. / Abashidze, M. / Conover, K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionFeb 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Succinylglutamate desuccinylase
B: Succinylglutamate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8714
Polymers75,7402
Non-polymers1312
Water7,602422
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.950, 39.435, 131.585
Angle α, β, γ (deg.)90.00, 94.74, 90.00
Int Tables number4
Space group name H-MP1211
Detailspossibly dimer

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Components

#1: Protein Succinylglutamate desuccinylase


Mass: 37870.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: ATCC 12472 / Gene: astE / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic
Keywords: Substitution of Met by Seleno-Met and addition of a C-tag (LEHHHHHH), AstE
References: UniProt: Q7NU26, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.22 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM MES (pH 6.0), 18% PEG 2K, 100 mM magnesium chloride, and 5 DTT. , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 85332 / Num. obs: 83796 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.052 / Net I/σ(I): 19.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 5 / Num. unique all: 8284 / Rsym value: 0.277 / % possible all: 96.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→29.95 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 398591.66 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 7580 9.8 %RANDOM
Rwork0.221 ---
all0.224 83796 --
obs0.221 77568 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.9201 Å2 / ksol: 0.341606 e/Å3
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1-5 Å20 Å27.45 Å2
2---4.84 Å20 Å2
3----0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4853 0 2 422 5277
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 1086 9.7 %
Rwork0.23 10151 -
obs-10151 78.9 %

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