[English] 日本語
Yorodumi
- PDB-4i3w: Structure of phosphonoacetaldehyde dehydrogenase in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i3w
TitleStructure of phosphonoacetaldehyde dehydrogenase in complex with gylceraldehyde-3-phosphate and cofactor NAD+
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 / 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
GLYCERALDEHYDE-3-PHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Phosphonoacetaldehyde dehydrogenase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)432,05223
Polymers426,0478
Non-polymers6,00415
Water30,2291678
1
A: Aldehyde dehydrogenase (NAD+)
F: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1796
Polymers106,5122
Non-polymers1,6674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-53 kcal/mol
Surface area32160 Å2
MethodPISA
2
B: Aldehyde dehydrogenase (NAD+)
C: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1796
Polymers106,5122
Non-polymers1,6674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-54 kcal/mol
Surface area32160 Å2
MethodPISA
3
D: Aldehyde dehydrogenase (NAD+)
E: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1796
Polymers106,5122
Non-polymers1,6674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-53 kcal/mol
Surface area32170 Å2
MethodPISA
4
G: Aldehyde dehydrogenase (NAD+)
H: Aldehyde dehydrogenase (NAD+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5155
Polymers106,5122
Non-polymers1,0043
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-48 kcal/mol
Surface area32310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.450, 172.706, 139.776
Angle α, β, γ (deg.)90.000, 106.900, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A AND (RESSEQ 12:484 )
21CHAIN B AND (RESSEQ 12:484 )
31CHAIN C AND (RESSEQ 12:484 )
41CHAIN D AND (RESSEQ 12:484 )
51CHAIN E AND (RESSEQ 12:484 )
61CHAIN F AND (RESSEQ 12:484 )
71CHAIN G AND (RESSEQ 12:484 )
81CHAIN H AND (RESSEQ 12:484 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A AND (RESSEQ 12:484 )A12 - 484
211CHAIN B AND (RESSEQ 12:484 )B12 - 484
311CHAIN C AND (RESSEQ 12:484 )C12 - 484
411CHAIN D AND (RESSEQ 12:484 )D12 - 484
511CHAIN E AND (RESSEQ 12:484 )E12 - 484
611CHAIN F AND (RESSEQ 12:484 )F12 - 484
711CHAIN G AND (RESSEQ 12:484 )G12 - 484
811CHAIN H AND (RESSEQ 12:484 )H12 - 484

-
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-G3H / GLYCERALDEHYDE-3-PHOSPHATE


Mass: 170.058 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1678 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG3350, pH 6.5, vapor diffusion, hanging drop, temperature 290K

-
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: 2.24→40 Å / Num. obs: 198176 / % possible obs: 97.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.109 / Χ2: 1.391 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.24-2.293.70.43197090.703196.3
2.29-2.333.80.41797850.712196.1
2.33-2.383.80.3897930.726196
2.38-2.423.80.34797800.727196.5
2.42-2.483.90.32498020.735196.5
2.48-2.533.90.28898420.765196.9
2.53-2.640.25398650.802197
2.6-2.6740.21498400.824197.1
2.67-2.754.10.19598570.851197
2.75-2.834.20.17598880.922197.3
2.83-2.944.40.15599200.969197.3
2.94-3.054.50.14298941.028197
3.05-3.194.70.12598371.124197
3.19-3.364.80.10898621.349196.8
3.36-3.5750.09798331.762196.5
3.57-3.855.10.09298612.255196.7
3.85-4.235.20.083100032.617198.1
4.23-4.845.50.071101942.657199.6
4.84-6.15.90.065102471.9111100
6.1-405.80.05103641.9811100

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
PHENIX1.7.1_743refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→24.969 Å / Occupancy max: 1 / Occupancy min: 0.18 / SU ML: 0.7 / σ(F): 1.36 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 9985 5.04 %
Rwork0.2038 --
obs0.2061 198011 97.08 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.026 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 98.58 Å2 / Biso mean: 24.6152 Å2 / Biso min: 4.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.131 Å20 Å20.1292 Å2
2--0.2478 Å20 Å2
3----0.1168 Å2
Refinement stepCycle: LAST / Resolution: 2.24→24.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29008 0 277 1678 30963
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3626X-RAY DIFFRACTIONPOSITIONAL0.1
12B3626X-RAY DIFFRACTIONPOSITIONAL0.1
13C3626X-RAY DIFFRACTIONPOSITIONAL0.107
14D3626X-RAY DIFFRACTIONPOSITIONAL0.071
15E3626X-RAY DIFFRACTIONPOSITIONAL0.088
16F3626X-RAY DIFFRACTIONPOSITIONAL0.09
17G3626X-RAY DIFFRACTIONPOSITIONAL0.098
18H3626X-RAY DIFFRACTIONPOSITIONAL0.115

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more