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- PDB-4i3t: Structure of phosphonoacetaldehyde dehydrogenase in the apo state -

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Basic information

Entry
Database: PDB / ID: 4i3t
TitleStructure of phosphonoacetaldehyde dehydrogenase in the apo state
ComponentsAldehyde dehydrogenase (NAD+)
KeywordsOXIDOREDUCTASE / aldehyde dehydrogenase / phosphonate catabolism
Function / homology
Function and homology information


lactaldehyde dehydrogenase (NAD+) activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With 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 ...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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phosphonoacetaldehyde dehydrogenase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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)426,80716
Polymers426,0478
Non-polymers7608
Water41,9572329
1
A: Aldehyde dehydrogenase (NAD+)
F: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7024
Polymers106,5122
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-45 kcal/mol
Surface area32500 Å2
MethodPISA
2
B: Aldehyde dehydrogenase (NAD+)
hetero molecules

H: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7024
Polymers106,5122
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area5380 Å2
ΔGint-46 kcal/mol
Surface area32470 Å2
MethodPISA
3
C: Aldehyde dehydrogenase (NAD+)
E: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7024
Polymers106,5122
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-45 kcal/mol
Surface area32440 Å2
MethodPISA
4
D: Aldehyde dehydrogenase (NAD+)
hetero molecules

G: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7024
Polymers106,5122
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y+1/2,-z+11
Buried area5430 Å2
ΔGint-46 kcal/mol
Surface area32380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.720, 172.790, 142.580
Angle α, β, γ (deg.)90.000, 107.570, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A AND (RESSEQ 11:484 )
21CHAIN B AND (RESSEQ 11:484 )
31CHAIN C AND (RESSEQ 11:484 )
41CHAIN D AND (RESSEQ 11:484 )
51CHAIN E AND (RESSEQ 11:484 )
61CHAIN F AND (RESSEQ 11:484 )
71CHAIN G AND (RESSEQ 11:484 )
81CHAIN H AND (RESSEQ 11:484 )

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: TRP / End label comp-ID: TRP / Auth seq-ID: 11 - 484 / Label seq-ID: 14 - 487

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1CHAIN A AND (RESSEQ 11:484 )AA
2CHAIN B AND (RESSEQ 11:484 )BB
3CHAIN C AND (RESSEQ 11:484 )CC
4CHAIN D AND (RESSEQ 11:484 )DD
5CHAIN E AND (RESSEQ 11:484 )EE
6CHAIN F AND (RESSEQ 11:484 )FF
7CHAIN G AND (RESSEQ 11:484 )GG
8CHAIN H AND (RESSEQ 11:484 )HH

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Components

#1: Protein
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2329 / 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: 2.64 Å3/Da / Density % sol: 53.38 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→24.871 Å / Num. obs: 246726 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.638 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 7.47
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.20.551.66915029312187.9
2.2-2.30.4882.8311151926864196.6
2.3-2.40.3763.629474122596196.8
2.4-2.50.3164.238113719184196.9
2.5-2.80.2145.9918171842546197.2
2.8-30.1528.28464919715197.5
3-3.50.11310.7213746231841197.8
3.5-4.30.08813.8610785625089197.9
4.3-5.30.08215.285900213739198.2
5.3-70.08414.8383398959198.3
7-500.08115.93285436881197.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.1→24.871 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8306 / SU ML: 0.64 / σ(F): 1.99 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 12329 5 %
Rwork0.1976 --
obs0.1996 246582 96.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.106 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso max: 112.6 Å2 / Biso mean: 33.1813 Å2 / Biso min: 8.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.1448 Å2-0 Å2-0.0528 Å2
2---0.2875 Å20 Å2
3---0.4323 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29096 0 40 2329 31465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00929758
X-RAY DIFFRACTIONf_angle_d1.14740478
X-RAY DIFFRACTIONf_chiral_restr0.0774694
X-RAY DIFFRACTIONf_plane_restr0.0055276
X-RAY DIFFRACTIONf_dihedral_angle_d14.4611074
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3621X-RAY DIFFRACTIONPOSITIONAL0.074
12B3621X-RAY DIFFRACTIONPOSITIONAL0.074
13C3629X-RAY DIFFRACTIONPOSITIONAL0.053
14D3629X-RAY DIFFRACTIONPOSITIONAL0.066
15E3629X-RAY DIFFRACTIONPOSITIONAL0.066
16F3637X-RAY DIFFRACTIONPOSITIONAL0.066
17G3629X-RAY DIFFRACTIONPOSITIONAL0.055
18H3637X-RAY DIFFRACTIONPOSITIONAL0.063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.12390.34963100.32295890620072
2.1239-2.14880.33033820.2987259764190
2.1488-2.1750.33044050.28697689809495
2.175-2.20260.34060.27397704811096
2.2026-2.23150.32164110.26417810822197
2.2315-2.26210.31554130.26097846825997
2.2621-2.29440.33014100.24967803821397
2.2944-2.32860.30414150.25437888830397
2.3286-2.36490.29654130.23767838825197
2.3649-2.40370.28414120.2317831824397
2.4037-2.44510.2784110.22837815822697
2.4451-2.48950.28234140.22857850826497
2.4895-2.53740.26914140.22387868828297
2.5374-2.58910.28484160.22437904832097
2.5891-2.64530.26114140.21887876829097
2.6453-2.70680.27864160.21967894831097
2.7068-2.77440.26474160.21147902831897
2.7744-2.84930.26724150.21597897831297
2.8493-2.9330.25724150.20817889830498
2.933-3.02750.25954180.21277945836397
3.0275-3.13560.28044180.21357930834898
3.1356-3.26080.23354160.19897912832898
3.2608-3.40890.22824210.19517997841898
3.4089-3.58810.2074180.18127934835298
3.5881-3.81220.21944200.18277984840498
3.8122-4.10530.19764190.16037962838198
4.1053-4.51620.1894210.14858007842898
4.5162-5.16460.17064210.14517981840298
5.1646-6.48770.21574240.17748072849698
6.4877-24.87270.16284250.15668076850198

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