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- PDB-4i3x: Structure of phosphonoacetaldehyde dehydrogenase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4i3x
TitleStructure of phosphonoacetaldehyde dehydrogenase in complex with phosphonoacetate 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 / PHOSPHONOACETIC ACID / Phosphonoacetaldehyde dehydrogenase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)432,47524
Polymers426,0478
Non-polymers6,42816
Water51,7572873
1
A: Aldehyde dehydrogenase (NAD+)
B: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1196
Polymers106,5122
Non-polymers1,6074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-48 kcal/mol
Surface area32210 Å2
MethodPISA
2
C: Aldehyde dehydrogenase (NAD+)
hetero molecules

E: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1196
Polymers106,5122
Non-polymers1,6074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area7220 Å2
ΔGint-51 kcal/mol
Surface area32140 Å2
MethodPISA
3
D: Aldehyde dehydrogenase (NAD+)
H: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1196
Polymers106,5122
Non-polymers1,6074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-48 kcal/mol
Surface area32300 Å2
MethodPISA
4
F: Aldehyde dehydrogenase (NAD+)
hetero molecules

G: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1196
Polymers106,5122
Non-polymers1,6074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area7370 Å2
ΔGint-49 kcal/mol
Surface area31930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.162, 172.765, 142.596
Angle α, β, γ (deg.)90.000, 107.280, 90.000
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.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-PAE / PHOSPHONOACETIC ACID


Mass: 140.032 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H5O5P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2873 / 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: 2.63 Å3/Da / Density % sol: 53.18 %
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: 2.07→136.16 Å / Num. obs: 250280 / % possible obs: 94.1 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.098 / Χ2: 1.164 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.07-2.114.70.56599210.902174.9
2.11-2.145.10.546105800.901179.8
2.14-2.195.60.491110420.9183.3
2.19-2.2360.457113910.904185.9
2.23-2.286.30.404117750.894188.6
2.28-2.336.40.367121630.894191.5
2.33-2.396.60.331124980.894194.2
2.39-2.456.70.299128130.899196.5
2.45-2.536.90.266129200.888197.5
2.53-2.6170.218129940.925197.9
2.61-2.77.10.185131360.943198.5
2.7-2.817.10.154130950.964198.6
2.81-2.947.30.13131371.039198.8
2.94-3.097.30.114131971.122199
3.09-3.297.40.095132191.316199.2
3.29-3.547.50.074132071.503199.3
3.54-3.97.60.059132471.589199.5
3.9-4.467.70.049133001.672199.6
4.46-5.627.70.044133631.603199.7
5.62-507.50.04132821.683198.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.388 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 12509 5 %RANDOM
Rwork0.1616 ---
obs0.1643 250226 93.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.22 Å2 / Biso mean: 27.3974 Å2 / Biso min: 4.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20.03 Å2
2---0.06 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.07→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29163 0 416 2873 32452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01930187
X-RAY DIFFRACTIONr_angle_refined_deg2.0661.99141131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70653795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.10823.4831246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.763154966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.58215246
X-RAY DIFFRACTIONr_chiral_restr0.1380.24767
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02122650
LS refinement shellResolution: 2.07→2.125 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 715 -
Rwork0.267 14013 -
all-14728 -
obs--75.26 %

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