[English] 日本語
Yorodumi
- PDB-7r5t: CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7r5t
TitleCRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT F254I COMPLEXED WITH FE, NADH, AND GLYCEROL
ComponentsLactaldehyde reductase
KeywordsOXIDOREDUCTASE / FucO / NADH / Dehydrogenase / aldehyde reductase
Function / homology
Function and homology information


lactaldehyde reductase / R-lactaldehyde reductase activity / S-lactaldehyde reductase activity / fucose catabolic process / alcohol dehydrogenase (NAD+) activity / metal ion binding
Similarity search - Function
Lactaldehyde reductase / Iron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / : / Fe-containing alcohol dehydrogenase family, C-terminal / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / : / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Lactaldehyde reductase
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSridhar, S. / Kiema, T.R. / Wierenga, R. / Widersten, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Other privateOlle Engkvist Byggmastare Foundation - 194-0638 Sweden
CitationJournal: Febs J. / Year: 2023
Title: Structures of lactaldehyde reductase, FucO, link enzyme activity to hydrogen bond networks and conformational dynamics.
Authors: Zavarise, A. / Sridhar, S. / Kiema, T.R. / Wierenga, R.K. / Widersten, M.
History
DepositionFeb 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Lactaldehyde reductase
BBB: Lactaldehyde reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,36116
Polymers83,0632
Non-polymers3,29814
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.559, 54.329, 101.795
Angle α, β, γ (deg.)90.000, 99.970, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AAABBB

#1: Protein Lactaldehyde reductase / Propanediol oxidoreductase


Mass: 41531.320 Da / Num. of mol.: 2 / Mutation: F254I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: fucO, Z4116, ECs3659
Production host: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Strain (production host): XL1-Blue / References: UniProt: P0A9S2, lactaldehyde reductase

-
Non-polymers , 5 types, 253 molecules

#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Magnesium chloride hexahydrate; 0.1M Bis-Tris, pH 5.5; 25% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.85→61.841 Å / Num. obs: 64213 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.5 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.056 / Net I/σ(I): 7.3
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3986 / CC1/2: 0.85 / Rpim(I) all: 0.273 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RRM

1rrm


Resolution: 1.85→61.841 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.725 / SU ML: 0.108 / Cross valid method: FREE R-VALUE / ESU R: 0.141 / ESU R Free: 0.129
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2154 3176 4.948 %
Rwork0.1824 61014 -
all0.184 --
obs-64190 99.852 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.386 Å2
Baniso -1Baniso -2Baniso -3
1--2.815 Å20 Å2-0.794 Å2
2--3.146 Å20 Å2
3----0.049 Å2
Refinement stepCycle: LAST / Resolution: 1.85→61.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5692 0 210 239 6141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0136046
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175732
X-RAY DIFFRACTIONr_angle_refined_deg1.31.6438256
X-RAY DIFFRACTIONr_angle_other_deg1.2541.5813201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4365776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75822.721272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.21515928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.281534
X-RAY DIFFRACTIONr_chiral_restr0.0610.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026838
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021262
X-RAY DIFFRACTIONr_nbd_refined0.1960.21220
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1660.25258
X-RAY DIFFRACTIONr_nbtor_refined0.1480.22921
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.22622
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2265
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.27
X-RAY DIFFRACTIONr_nbd_other0.1570.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0750.23
X-RAY DIFFRACTIONr_mcbond_it1.332.6643074
X-RAY DIFFRACTIONr_mcbond_other1.332.6633073
X-RAY DIFFRACTIONr_mcangle_it2.033.9913842
X-RAY DIFFRACTIONr_mcangle_other2.033.9923843
X-RAY DIFFRACTIONr_scbond_it1.7712.9352972
X-RAY DIFFRACTIONr_scbond_other1.7712.9362973
X-RAY DIFFRACTIONr_scangle_it2.8554.2874408
X-RAY DIFFRACTIONr_scangle_other2.8544.2884409
X-RAY DIFFRACTIONr_lrange_it4.01532.2876583
X-RAY DIFFRACTIONr_lrange_other3.99332.2286555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.2792650.2684453X-RAY DIFFRACTION99.9153
1.898-1.950.2852040.2514412X-RAY DIFFRACTION99.9567
1.95-2.0070.2512440.2464230X-RAY DIFFRACTION99.9107
2.007-2.0680.2562120.2264107X-RAY DIFFRACTION99.8844
2.068-2.1360.2152100.2044006X-RAY DIFFRACTION99.787
2.136-2.2110.2481920.1953889X-RAY DIFFRACTION99.9265
2.211-2.2940.2222200.1963698X-RAY DIFFRACTION99.949
2.294-2.3880.2031700.183646X-RAY DIFFRACTION99.6605
2.388-2.4940.2331910.1793428X-RAY DIFFRACTION99.7794
2.494-2.6160.251470.1833335X-RAY DIFFRACTION99.9139
2.616-2.7570.2091740.183153X-RAY DIFFRACTION99.6406
2.757-2.9240.2291650.1782952X-RAY DIFFRACTION99.8399
2.924-3.1260.2411280.1852829X-RAY DIFFRACTION100
3.126-3.3760.1991340.172626X-RAY DIFFRACTION99.9638
3.376-3.6980.191410.1622401X-RAY DIFFRACTION99.9607
3.698-4.1340.191050.1512211X-RAY DIFFRACTION99.6987
4.134-4.7720.178890.1481934X-RAY DIFFRACTION99.5081
4.772-5.8410.198860.1751660X-RAY DIFFRACTION99.8856
5.841-8.2470.185710.1811284X-RAY DIFFRACTION100
8.247-61.8410.181280.172760X-RAY DIFFRACTION99.4949

+
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