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- PDB-3rh9: The crystal structure of oxidoreductase from Marinobacter aquaeolei -

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Basic information

Entry
Database: PDB / ID: 3rh9
TitleThe crystal structure of oxidoreductase from Marinobacter aquaeolei
ComponentsSuccinate-semialdehyde dehydrogenase (NAD(P)(+))
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / ABM20716.1
Function / homology
Function and homology information


succinate-semialdehyde dehydrogenase [NAD(P)+] / succinate-semialdehyde dehydrogenase [NAD(P)+] activity
Similarity search - Function
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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal ...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 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
Succinate-semialdehyde dehydrogenase (NAD(P)(+))
Similarity search - Component
Biological speciesMarinobacter aquaeolei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.63 Å
AuthorsZhang, Z. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: The crystal structure of oxidoreductase from Marinobacter aquaeolei
Authors: Zhang, Z. / Almo, S.C. / Swaminathan, S.
History
DepositionApr 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Succinate-semialdehyde dehydrogenase (NAD(P)(+))
B: Succinate-semialdehyde dehydrogenase (NAD(P)(+))


Theoretical massNumber of molelcules
Total (without water)111,5902
Polymers111,5902
Non-polymers00
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-28 kcal/mol
Surface area32900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.483, 102.477, 144.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Succinate-semialdehyde dehydrogenase (NAD(P)(+))


Mass: 55795.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinobacter aquaeolei (bacteria) / Strain: VT8 / Gene: Maqu_3647 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) rip
References: UniProt: A1U6U7, succinate-semialdehyde dehydrogenase [NAD(P)+]
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1 M Citric acid pH 3.5, 25% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 30524 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 35.9
Reflection shellResolution: 2.63→2.72 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 5.3 / Num. unique all: 2998 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.63→49.317 Å / SU ML: 0.37 / Isotropic thermal model: Isotropic / σ(F): 9.43 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.2517 2000 6.67 %
Rwork0.1868 --
obs0.1911 30004 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 8.296 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso mean: 21.58 Å2
Baniso -1Baniso -2Baniso -3
1--4.219 Å20 Å20 Å2
2--3.0635 Å2-0 Å2
3---1.1554 Å2
Refinement stepCycle: LAST / Resolution: 2.63→49.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7248 0 0 259 7507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097417
X-RAY DIFFRACTIONf_angle_d1.15310047
X-RAY DIFFRACTIONf_dihedral_angle_d17.6642707
X-RAY DIFFRACTIONf_chiral_restr0.0731105
X-RAY DIFFRACTIONf_plane_restr0.0051326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6301-2.69590.3131360.22881897X-RAY DIFFRACTION94
2.6959-2.76880.29221370.22711929X-RAY DIFFRACTION97
2.7688-2.85020.31911400.20541958X-RAY DIFFRACTION97
2.8502-2.94220.2811380.22321943X-RAY DIFFRACTION98
2.9422-3.04730.31051410.22711971X-RAY DIFFRACTION98
3.0473-3.16930.33311410.2121967X-RAY DIFFRACTION98
3.1693-3.31360.23871430.20552003X-RAY DIFFRACTION99
3.3136-3.48820.30991420.181994X-RAY DIFFRACTION99
3.4882-3.70670.20811440.17552018X-RAY DIFFRACTION99
3.7067-3.99280.25531450.15472010X-RAY DIFFRACTION99
3.9928-4.39430.18621440.14662031X-RAY DIFFRACTION99
4.3943-5.02970.18851450.12822032X-RAY DIFFRACTION99
5.0297-6.33480.21231500.15332084X-RAY DIFFRACTION99
6.3348-49.32520.19251540.1672167X-RAY DIFFRACTION99

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