[English] 日本語
Yorodumi
- PDB-6scg: Structure of AdhE form 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6scg
TitleStructure of AdhE form 1
ComponentsAldehyde-alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / aldehyde alcohol dehydrogenase
Function / homology
Function and homology information


ethanol biosynthetic process / mixed acid fermentation / alcohol dehydrogenase (NAD+) activity, iron-dependent / acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / carbon utilization / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / ferrous iron binding / protein homooligomerization ...ethanol biosynthetic process / mixed acid fermentation / alcohol dehydrogenase (NAD+) activity, iron-dependent / acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / carbon utilization / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / ferrous iron binding / protein homooligomerization / response to oxidative stress / membrane / identical protein binding / cytosol
Similarity search - Function
Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Bifunctional aldehyde-alcohol dehydrogenase AdhE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsLovering, A.L. / Bragginton, E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: High-resolution structure of the alcohol dehydrogenase domain of the bifunctional bacterial enzyme AdhE.
Authors: Azmi, L. / Bragginton, E.C. / Cadby, I.T. / Byron, O. / Roe, A.J. / Lovering, A.L. / Gabrielsen, M.
History
DepositionJul 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 2.0Mar 17, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aldehyde-alcohol dehydrogenase
B: Aldehyde-alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,77411
Polymers99,7902
Non-polymers1,9849
Water11,584643
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-93 kcal/mol
Surface area29660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.138, 97.138, 233.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Components on special symmetry positions
IDModelComponents
11B-1384-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
32

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 450 through 522 or resid 524...A450 - 522
121(chain 'A' and (resid 450 through 522 or resid 524...A524 - 533
131(chain 'A' and (resid 450 through 522 or resid 524...A535 - 545
141(chain 'A' and (resid 450 through 522 or resid 524...A548 - 576
151(chain 'A' and (resid 450 through 522 or resid 524...A581 - 754
161(chain 'A' and (resid 450 through 522 or resid 524...A769 - 770
171(chain 'A' and (resid 450 through 522 or resid 524...A773 - 789
181(chain 'A' and (resid 450 through 522 or resid 524...A791 - 832
191(chain 'A' and (resid 450 through 522 or resid 524...A834 - 869
1101(chain 'A' and (resid 450 through 522 or resid 524...A901
2111(chain 'B' and (resid 450 through 522 or resid 524...B450 - 522
2121(chain 'B' and (resid 450 through 522 or resid 524...B524 - 533
2131(chain 'B' and (resid 450 through 522 or resid 524...B535 - 545
2141(chain 'B' and (resid 450 through 522 or resid 524...B548 - 576
2151(chain 'B' and (resid 450 through 522 or resid 524...B581 - 754
2161(chain 'B' and (resid 450 through 522 or resid 524...B769 - 770
2171(chain 'B' and (resid 450 through 522 or resid 524...B773 - 789
2181(chain 'B' and (resid 450 through 522 or resid 524...B791 - 832
2191(chain 'B' and (resid 450 through 522 or resid 524...B834 - 869
2201(chain 'B' and (resid 450 through 522 or resid 524...B901

NCS ensembles :
ID
1
2

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Aldehyde-alcohol dehydrogenase


Mass: 49895.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: adhE, ana, b1241, JW1228 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A9Q7, alcohol dehydrogenase, acetaldehyde dehydrogenase (acetylating)

-
Non-polymers , 6 types, 652 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MES pH 6.0 0.2M Li sulphate 20% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9174 Å / Relative weight: 1
ReflectionResolution: 1.65→89.68 Å / Num. obs: 134736 / % possible obs: 100 % / Redundancy: 17.7 % / Biso Wilson estimate: 23.37 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.027 / Rrim(I) all: 0.111 / Net I/σ(I): 19.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.65-1.6814.22.0569305165640.5770.5582.1321.499.4
9.04-50.0215.80.031560899010.0080.03174.199.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.3.6data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZDR

3zdr


Resolution: 1.65→50.02 Å / SU ML: 0.176 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.896
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1805 6731 5 %RANDOM
Rwork0.1551 127845 --
obs0.1564 134576 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.43 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6250 0 121 643 7014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01336566
X-RAY DIFFRACTIONf_angle_d1.28338926
X-RAY DIFFRACTIONf_chiral_restr0.08641004
X-RAY DIFFRACTIONf_plane_restr0.0061135
X-RAY DIFFRACTIONf_dihedral_angle_d13.48642384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.27362160.26014169X-RAY DIFFRACTION99.12
1.67-1.690.2572240.23624172X-RAY DIFFRACTION99.86
1.69-1.710.25872250.22124217X-RAY DIFFRACTION100
1.71-1.730.25862270.20924193X-RAY DIFFRACTION99.95
1.73-1.750.21562110.19814206X-RAY DIFFRACTION99.91
1.75-1.780.29172310.25684199X-RAY DIFFRACTION99.98
1.78-1.80.25622120.25424229X-RAY DIFFRACTION100
1.8-1.830.25912260.22864228X-RAY DIFFRACTION99.98
1.83-1.860.25272320.20114196X-RAY DIFFRACTION99.93
1.86-1.890.18392390.18214180X-RAY DIFFRACTION99.95
1.89-1.920.20262320.17224214X-RAY DIFFRACTION99.98
1.92-1.960.19282160.15534228X-RAY DIFFRACTION99.98
1.96-1.990.19822190.14744230X-RAY DIFFRACTION100
1.99-2.030.17052170.14714236X-RAY DIFFRACTION100
2.03-2.080.18882460.14944190X-RAY DIFFRACTION99.93
2.08-2.130.16722110.14964257X-RAY DIFFRACTION99.93
2.13-2.180.18172210.14474247X-RAY DIFFRACTION100
2.18-2.240.16722020.13414256X-RAY DIFFRACTION100
2.24-2.30.17332050.14194256X-RAY DIFFRACTION100
2.3-2.380.16192270.12614266X-RAY DIFFRACTION100
2.38-2.460.18312290.13474249X-RAY DIFFRACTION99.96
2.46-2.560.17152070.13364288X-RAY DIFFRACTION100
2.56-2.680.16652360.13824267X-RAY DIFFRACTION100
2.68-2.820.17642340.14474288X-RAY DIFFRACTION100
2.82-30.19012380.15224258X-RAY DIFFRACTION100
3-3.230.17992260.16034327X-RAY DIFFRACTION100
3.23-3.550.18772390.15424323X-RAY DIFFRACTION100
3.55-4.070.16172250.14414370X-RAY DIFFRACTION99.89
4.07-5.120.13362210.13464445X-RAY DIFFRACTION100
5.12-50.020.18292370.17264661X-RAY DIFFRACTION99.8

+
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