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- PDB-3ros: Crystal structure of NAD-dependent aldehyde dehydrogenase from La... -

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Basic information

Entry
Database: PDB / ID: 3ros
TitleCrystal structure of NAD-dependent aldehyde dehydrogenase from Lactobacillus acidophilus
ComponentsNAD-dependent aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / NYSGRC / PSI-BIOLOGY / Structural Genomics / New York Structural Genomics Research Consortium / succinic semialdehyde dehydrogenase / NAD dependent
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
NAD-dependent aldehyde dehydrogenases
Similarity search - Component
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å
AuthorsEswaramoorthy, S. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of NAD-dependent aldehyde dehydrogenase from Lactobacillus acidophilus
Authors: Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S.
History
DepositionApr 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 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: NAD-dependent aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1142
Polymers54,0181
Non-polymers961
Water3,819212
1
A: NAD-dependent aldehyde dehydrogenase
hetero molecules

A: NAD-dependent aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2284
Polymers108,0362
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5900 Å2
ΔGint-59 kcal/mol
Surface area33110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.000, 45.730, 96.378
Angle α, β, γ (deg.)90.00, 121.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NAD-dependent aldehyde dehydrogenase


Mass: 54018.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: ssdh, LBA1632 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q5FIM9, succinate-semialdehyde dehydrogenase [NAD(P)+]
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.8
Details: 25% PEG1500, 0.1M Citric Acid, 5mM Hexammine Cobalt(III)Chloride, pH 3.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. all: 40745 / Num. obs: 40745 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 11.7
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.253 / Num. unique all: 4042 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.88→42.41 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 92950.85 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED, BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2011 5 %RANDOM
Rwork0.192 ---
all0.208 39983 --
obs0.192 39983 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.3979 Å2 / ksol: 0.406438 e/Å3
Displacement parametersBiso mean: 13.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-1.67 Å2
2--1.65 Å20 Å2
3----1.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.01 Å
Refinement stepCycle: LAST / Resolution: 1.88→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3532 0 5 212 3749
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 1.88→2 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.217 348 5.4 %
Rwork0.191 6102 -
obs-6450 95.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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