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- PDB-4i3u: Structure of phosphonoacetaldehyde dehydrogenase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4i3u
TitleStructure of phosphonoacetaldehyde dehydrogenase in complex with phosphonoacetaldehyde
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
PHOSPHONOACETALDEHYDE / Phosphonoacetaldehyde dehydrogenase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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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)427,04016
Polymers426,0478
Non-polymers9928
Water34,5171916
1
A: Aldehyde dehydrogenase (NAD+)
D: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7604
Polymers106,5122
Non-polymers2482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-39 kcal/mol
Surface area32140 Å2
MethodPISA
2
B: Aldehyde dehydrogenase (NAD+)
hetero molecules

G: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7604
Polymers106,5122
Non-polymers2482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
Buried area5590 Å2
ΔGint-39 kcal/mol
Surface area32130 Å2
MethodPISA
3
C: Aldehyde dehydrogenase (NAD+)
hetero molecules

E: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7604
Polymers106,5122
Non-polymers2482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
Buried area5600 Å2
ΔGint-40 kcal/mol
Surface area32060 Å2
MethodPISA
4
F: Aldehyde dehydrogenase (NAD+)
H: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7604
Polymers106,5122
Non-polymers2482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-39 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.350, 172.880, 138.970
Angle α, β, γ (deg.)90.00, 106.73, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 12:214 OR RESSEQ 216:270 OR RESSEQ 272:484 )
211CHAIN B AND (RESSEQ 12:214 OR RESSEQ 216:270 OR RESSEQ 272:484 )
311CHAIN C AND (RESSEQ 12:214 OR RESSEQ 216:270 OR RESSEQ 272:484 )
411CHAIN D AND (RESSEQ 12:214 OR RESSEQ 216:270 OR RESSEQ 272:484 )
511CHAIN E AND (RESSEQ 12:214 OR RESSEQ 216:270 OR RESSEQ 272:484 )
611CHAIN F AND (RESSEQ 12:214 OR RESSEQ 216:270 OR RESSEQ 272:484 )
711CHAIN G AND (RESSEQ 12:214 OR RESSEQ 216:270 OR RESSEQ 272:484 )
811CHAIN H AND (RESSEQ 12:214 OR RESSEQ 216:270 OR RESSEQ 272:484 )

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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-POA / PHOSPHONOACETALDEHYDE


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


Mass: 18.015 Da / Num. of mol.: 1916 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
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: 2.1→39.111 Å / Num. obs: 236736 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.36
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.20.5361.64190.3
2.2-2.30.4282.21194.8
2.3-2.50.3522.94197.4
2.5-2.80.2244.97198.8
2.8-3.10.1497.76198.8
3.1-3.50.08912.54198.3
3.5-4.80.04522.44197.3
4.8-5.50.03625.96197
5.5-70.03525.4196.7
7-500.02136.86194.2

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
REFMACrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→39.111 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.6 / σ(F): 1.99 / Phase error: 25.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 11836 5 %
Rwork0.2096 --
obs0.2118 236727 96.59 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.871 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0818 Å20 Å20.0163 Å2
2--0.0949 Å2-0 Å2
3----0.1767 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29008 0 56 1916 30980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01629638
X-RAY DIFFRACTIONf_angle_d1.56740314
X-RAY DIFFRACTIONf_dihedral_angle_d14.83711014
X-RAY DIFFRACTIONf_chiral_restr0.0874680
X-RAY DIFFRACTIONf_plane_restr0.0095246
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3613X-RAY DIFFRACTIONPOSITIONAL
12B3613X-RAY DIFFRACTIONPOSITIONAL0.113
13C3613X-RAY DIFFRACTIONPOSITIONAL0.143
14D3613X-RAY DIFFRACTIONPOSITIONAL0.13
15E3613X-RAY DIFFRACTIONPOSITIONAL0.136
16F3613X-RAY DIFFRACTIONPOSITIONAL0.108
17G3613X-RAY DIFFRACTIONPOSITIONAL0.127
18H3613X-RAY DIFFRACTIONPOSITIONAL0.132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.34753580.31946804X-RAY DIFFRACTION88
2.1239-2.14880.34723650.30976932X-RAY DIFFRACTION90
2.1488-2.1750.32653750.29367130X-RAY DIFFRACTION91
2.175-2.20260.34333740.29017107X-RAY DIFFRACTION93
2.2026-2.23160.31943840.28237295X-RAY DIFFRACTION94
2.2316-2.26210.31833870.26767349X-RAY DIFFRACTION95
2.2621-2.29440.29093880.26337367X-RAY DIFFRACTION96
2.2944-2.32870.32883930.26767483X-RAY DIFFRACTION96
2.3287-2.36510.31023960.25217518X-RAY DIFFRACTION97
2.3651-2.40380.31543950.24587511X-RAY DIFFRACTION97
2.4038-2.44530.30764010.24437615X-RAY DIFFRACTION98
2.4453-2.48970.27943980.2337561X-RAY DIFFRACTION98
2.4897-2.53760.29784040.23437668X-RAY DIFFRACTION99
2.5376-2.58940.2814020.22637642X-RAY DIFFRACTION99
2.5894-2.64570.28734030.21887655X-RAY DIFFRACTION99
2.6457-2.70720.29254040.22117676X-RAY DIFFRACTION99
2.7072-2.77490.28124040.21137677X-RAY DIFFRACTION99
2.7749-2.84990.2654020.20187632X-RAY DIFFRACTION99
2.8499-2.93380.27494040.20897680X-RAY DIFFRACTION99
2.9338-3.02840.26834060.2097726X-RAY DIFFRACTION99
3.0284-3.13660.2584020.21377629X-RAY DIFFRACTION99
3.1366-3.26210.25524020.20567646X-RAY DIFFRACTION99
3.2621-3.41050.22584020.18927642X-RAY DIFFRACTION98
3.4105-3.59020.24024000.18737584X-RAY DIFFRACTION98
3.5902-3.8150.23263980.18357568X-RAY DIFFRACTION98
3.815-4.10920.18954000.16617606X-RAY DIFFRACTION97
4.1092-4.52220.17893980.15387553X-RAY DIFFRACTION97
4.5222-5.17530.18543980.15967574X-RAY DIFFRACTION97
5.1753-6.51550.22433980.20027554X-RAY DIFFRACTION97
6.5155-39.1180.18793950.17497507X-RAY DIFFRACTION95

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