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- PDB-3ju8: Crystal Structure of Succinylglutamic Semialdehyde Dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 3ju8
TitleCrystal Structure of Succinylglutamic Semialdehyde Dehydrogenase from Pseudomonas aeruginosa.
ComponentsSuccinylglutamic semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / alpha-beta structure / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Arginine metabolism / NAD
Function / homology
Function and homology information


succinylglutamate-semialdehyde dehydrogenase / succinylglutamate-semialdehyde dehydrogenase activity / arginine catabolic process to succinate / arginine catabolic process to glutamate / arginine catabolic process
Similarity search - Function
Succinylglutamate-semialdehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain ...Succinylglutamate-semialdehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SUCCINIC ACID / N-succinylglutamate 5-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.82 Å
AuthorsKim, Y. / Li, H. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Succinylglutamic Semialdehyde Dehydrogenase from Pseudomonas aeruginosa
Authors: Kim, Y. / Li, H. / Buck, K. / Joachimiak, A.
History
DepositionSep 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinylglutamic semialdehyde dehydrogenase
B: Succinylglutamic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,04524
Polymers104,0002
Non-polymers3,04522
Water16,736929
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13650 Å2
ΔGint-167 kcal/mol
Surface area32940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.117, 48.033, 187.130
Angle α, β, γ (deg.)90.00, 107.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-773-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Succinylglutamic semialdehyde dehydrogenase / N-succinylglutamate 5-semialdehyde dehydrogenase / SGSD


Mass: 51999.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: aruD, astD, PA0898 / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: O50174, succinylglutamate-semialdehyde dehydrogenase

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Non-polymers , 7 types, 951 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 929 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M Magnesium sulfate 0.1 M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 19, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.82→32.78 Å / Num. all: 104456 / Num. obs: 104456 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 24.03 Å2 / Rsym value: 0.064 / Net I/σ(I): 12.5
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 4769 / Rsym value: 0.41 / % possible all: 91.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine: 1.4_138)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.82→32.775 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 20.38 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.196 5214 5 %random
Rwork0.158 ---
all0.16 104285 --
obs0.16 104285 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.845 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.2147 Å20 Å20.5274 Å2
2--13.0734 Å20 Å2
3----8.8587 Å2
Refinement stepCycle: LAST / Resolution: 1.82→32.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7228 0 187 929 8344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138121
X-RAY DIFFRACTIONf_angle_d1.46411141
X-RAY DIFFRACTIONf_dihedral_angle_d18.8163039
X-RAY DIFFRACTIONf_chiral_restr0.1021233
X-RAY DIFFRACTIONf_plane_restr0.0071481
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.82-1.88510.26485200.229695511007198
1.8851-1.96050.24095390.1923990810447100
1.9605-2.04970.21625320.1752983910372100
2.0497-2.15780.21834970.1582997610473100
2.1578-2.2930.19745340.1511991010444100
2.293-2.46990.18794880.1484988710375100
2.4699-2.71840.22175110.1632995210463100
2.7184-3.11150.21415550.1663997710532100
3.1115-3.91910.16945220.144199811050399
3.9191-32.78070.1655160.1414100901060698
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined0.5350.0313-0.20720.162-0.05640.6065-0.0130.0264-0.06050.01420.0136-0.02020.04170.06960.00060.112-0.01940.00940.0877-0.02670.127-8.716419.941433.2851
20.8764-0.02040.00140.20790.12290.5454-0.03390.3993-0.0458-0.04060.03670.0305-0.0285-0.0410.00550.1642-0.05580.00540.3165-0.03480.1445
Refinement TLS groupSelection details: chain B

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