[English] 日本語
Yorodumi
- PDB-1wnb: Escherichia coli YdcW gene product is a medium-chain aldehyde deh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wnb
TitleEscherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase (complexed with nadh and betaine aldehyde)
ComponentsPutative betaine aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / aldehyde dehydrogenase / NADH / flurorescence / kinetics
Function / homology
Function and homology information


: / L-lysine catabolic process / putrescine catabolic process / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / aldehyde dehydrogenase (NAD+) activity / NAD binding / protein homotetramerization / protein-containing complex ...: / L-lysine catabolic process / putrescine catabolic process / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / aldehyde dehydrogenase (NAD+) activity / NAD binding / protein homotetramerization / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Gamma-aminobutyraldehyde dehydrogenase / Aminobutyraldehyde 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 ...Gamma-aminobutyraldehyde dehydrogenase / Aminobutyraldehyde 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
BETAINE ALDEHYDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Gamma-aminobutyraldehyde dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGruez, A. / Roig-Zamboni, V. / Tegoni, M. / Cambillau, C.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure and Kinetics Identify Escherichia coli YdcW Gene Product as a Medium-chain Aldehyde Dehydrogenase
Authors: Gruez, A. / Roig-Zamboni, V. / Grisel, S. / Salomoni, A. / Valencia, C. / Campanacci, V. / Tegoni, M. / Cambillau, C.
History
DepositionJul 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Nov 6, 2013Group: Non-polymer description
Revision 1.4Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative betaine aldehyde dehydrogenase
B: Putative betaine aldehyde dehydrogenase
C: Putative betaine aldehyde dehydrogenase
D: Putative betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,4029
Polymers213,6384
Non-polymers2,7645
Water14,970831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23580 Å2
ΔGint-137 kcal/mol
Surface area57180 Å2
MethodPISA
2
B: Putative betaine aldehyde dehydrogenase
D: Putative betaine aldehyde dehydrogenase
hetero molecules

A: Putative betaine aldehyde dehydrogenase
C: Putative betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,4029
Polymers213,6384
Non-polymers2,7645
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area16370 Å2
ΔGint-97 kcal/mol
Surface area64390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.278, 168.895, 85.476
Angle α, β, γ (deg.)90.00, 90.65, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNHIS5AA2 - 47423 - 495
21GLNHIS5BB2 - 47423 - 495
31GLNHIS5CC2 - 47423 - 495
41GLNHIS5DD2 - 47423 - 495
12NADNAD4AF10011
22NADNAD4BG20011
32NADNAD4CH30011
42NADNAD4DI40011

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Putative betaine aldehyde dehydrogenase / YdcW aldehyde dehydrogenase / BADH


Mass: 53409.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pDEST / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P77674, betaine-aldehyde dehydrogenase
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-BTL / BETAINE ALDEHYDE / [FORMYLMETHYL]TRIMETHYL-AMMONIUM / N,N,N-TRIMETHYL AMMONIUM ACETALDEHYDE / Glycine betaine aldehyde


Mass: 102.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 831 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 289573 / Num. obs: 107590 / % possible obs: 93.7 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 2.7 % / Biso Wilson estimate: 22.213 Å2 / Rmerge(I) obs: 0.089
Reflection shellResolution: 2.2→2.32 Å / % possible all: 93.7

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→18 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.886 / SU B: 5.856 / SU ML: 0.151 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.27 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23853 8946 8.3 %RANDOM
Rwork0.18195 ---
all0.18663 107534 --
obs0.18663 98588 93.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.718 Å2
Baniso -1Baniso -2Baniso -3
1-2.49 Å20 Å2-0.46 Å2
2---1.61 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.2→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14300 0 183 831 15314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02114780
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.96920108
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82951892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1210.22280
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211127
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.27162
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.21047
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4360.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4660.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7651.59389
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.265215008
X-RAY DIFFRACTIONr_scbond_it2.39735391
X-RAY DIFFRACTIONr_scangle_it3.4224.55100
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3550medium positional0.170.5
12B3550medium positional0.170.5
13C3550medium positional0.160.5
14D3550medium positional0.160.5
21A44medium positional1.040.5
22B44medium positional0.90.5
23C44medium positional1.230.5
24D44medium positional2.190.5
11A3550medium thermal1.072
12B3550medium thermal1.142
13C3550medium thermal1.142
14D3550medium thermal1.12
21A44medium thermal1.532
22B44medium thermal1.292
23C44medium thermal1.632
24D44medium thermal1.732
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.242 604
Rwork0.182 6457
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.13350.0236-0.04330.3270.02580.61640.0086-0.03640.10630.0520.0254-0.0442-0.22260.1264-0.0340.0656-0.03650.03950.1669-0.03060.132965.51584.3663.883
20.15930.09290.0670.40770.00250.46810.014-0.0266-0.07460.06040.00190.02110.1861-0.0189-0.01590.05460.00220.00940.1307-0.00940.118548.35339.14360.817
30.1351-0.1069-0.01170.4155-0.15840.69890.0229-0.00470.0551-0.0259-0.0010.1066-0.1137-0.1117-0.0220.01250.01470.0350.1228-0.00290.116738.31578.80841.198
40.2291-0.10140.02570.30970.01870.45530.0140.0323-0.078-0.0547-0.0139-0.08820.13240.198100.05030.0130.00370.1845-0.02020.145875.46747.97638.864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 47422 - 495
2X-RAY DIFFRACTION2BB1 - 47422 - 495
3X-RAY DIFFRACTION3CC1 - 47422 - 495
4X-RAY DIFFRACTION4DD1 - 47422 - 495

+
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://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