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- PDB-4i3v: Structure of phosphonoacetaldehyde dehydrogenase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4i3v
TitleStructure of phosphonoacetaldehyde dehydrogenase in complex with phosphonoacetaldehyde and cofactor NAD+
ComponentsAldehyde dehydrogenase (NAD+)Aldehyde dehydrogenase (NAD+)
KeywordsOXIDOREDUCTASE / aldehyde dehydrogenase / phosphonate catabolism
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
Putative phosphonoacetaldehyde 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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal ...Putative phosphonoacetaldehyde 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 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 / PHOSPHONOACETALDEHYDE / Phosphonoacetaldehyde dehydrogenase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNair, S.K. / Agarwal, V.
CitationJournal: Chem.Biol. / Year: 2014
Title: Structure and function of phosphonoacetaldehyde dehydrogenase: the missing link in phosphonoacetate formation.
Authors: Agarwal, V. / Peck, S.C. / Chen, J.H. / Borisova, S.A. / Chekan, J.R. / van der Donk, W.A. / Nair, S.K.
History
DepositionNov 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldehyde dehydrogenase (NAD+)
B: Aldehyde dehydrogenase (NAD+)
C: Aldehyde dehydrogenase (NAD+)
D: Aldehyde dehydrogenase (NAD+)
E: Aldehyde dehydrogenase (NAD+)
F: Aldehyde dehydrogenase (NAD+)
G: Aldehyde dehydrogenase (NAD+)
H: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)431,68423
Polymers426,0478
Non-polymers5,63615
Water46,3172571
1
A: Aldehyde dehydrogenase (NAD+)
C: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0876
Polymers106,5122
Non-polymers1,5754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-40 kcal/mol
Surface area32180 Å2
MethodPISA
2
B: Aldehyde dehydrogenase (NAD+)
F: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0876
Polymers106,5122
Non-polymers1,5754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-43 kcal/mol
Surface area32140 Å2
MethodPISA
3
D: Aldehyde dehydrogenase (NAD+)
E: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0876
Polymers106,5122
Non-polymers1,5754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-44 kcal/mol
Surface area32190 Å2
MethodPISA
4
G: Aldehyde dehydrogenase (NAD+)
H: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4235
Polymers106,5122
Non-polymers9113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-35 kcal/mol
Surface area32250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.744, 172.128, 140.056
Angle α, β, γ (deg.)90.00, 107.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aldehyde dehydrogenase (NAD+) / Aldehyde dehydrogenase (NAD+)


Mass: 53255.922 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: phnY, RB0979, SM_b21539 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q92UV7, aldehyde dehydrogenase (NAD+)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-POA / PHOSPHONOACETALDEHYDE


Mass: 124.032 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H5O4P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2571 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG3350, pH 6.5, vapor diffusion, hanging drop, temperature 290K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 286921 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.127 / Χ2: 1.16 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.036.20.843142220.826199.6
2.03-2.076.30.768142670.852199.6
2.07-2.116.30.659143130.856199.7
2.11-2.156.40.6143350.87199.8
2.15-2.26.40.525142720.887199.8
2.2-2.256.50.458142500.899199.8
2.25-2.316.50.394143900.917199.9
2.31-2.376.60.366143100.9291100
2.37-2.446.70.334142800.9511100
2.44-2.526.70.291143520.947199.9
2.52-2.616.80.24143470.999199.9
2.61-2.716.80.195143381.0061100
2.71-2.846.90.164143331.0321100
2.84-2.996.90.141143761.131100
2.99-3.1770.123143711.2931100
3.17-3.4270.097143731.5641100
3.42-3.7670.073143771.6771100
3.76-4.3170.055144231.7261100
4.31-5.4270.048143921.7411100
5.42-406.80.047146001.8351100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
PHENIX1.7.1_743refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.503 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.59 / σ(F): 1.34 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 14498 5.05 %
Rwork0.1822 --
obs0.1846 286857 99.87 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.199 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 84.36 Å2 / Biso mean: 27.2095 Å2 / Biso min: 10.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.0068 Å20 Å20.0069 Å2
2--0.0414 Å20 Å2
3----0.0347 Å2
Refinement stepCycle: LAST / Resolution: 2→39.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29008 0 245 2571 31824

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