[English] 日本語
Yorodumi
- PDB-7v1q: Leifsonia Alcohol Dehydrogenases LnADH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v1q
TitleLeifsonia Alcohol Dehydrogenases LnADH
ComponentsAlcohol Dehydrogenases
KeywordsBIOSYNTHETIC PROTEIN / Alcohol / Dehydrogenases
Function / homologyISOPROPYL ALCOHOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesLeifsonia antarctica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 Å
AuthorsSong, Y. / Qu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970054 China
CitationJournal: Chembiochem / Year: 2021
Title: Engineering Leifsonia Alcohol Dehydrogenase for Thermostability and Catalytic Efficiency by Enhancing Subunit Interactions.
Authors: Zhu, L. / Song, Y. / Chang, C. / Ma, H. / Yang, L. / Deng, Z. / Deng, W. / Qu, X.
History
DepositionAug 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alcohol Dehydrogenases
B: Alcohol Dehydrogenases
C: Alcohol Dehydrogenases
D: Alcohol Dehydrogenases
E: Alcohol Dehydrogenases
F: Alcohol Dehydrogenases
G: Alcohol Dehydrogenases
H: Alcohol Dehydrogenases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,72537
Polymers202,0868
Non-polymers6,63829
Water17,727984
1
A: Alcohol Dehydrogenases
B: Alcohol Dehydrogenases
D: Alcohol Dehydrogenases
E: Alcohol Dehydrogenases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,46020
Polymers101,0434
Non-polymers3,41716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19460 Å2
ΔGint-267 kcal/mol
Surface area28350 Å2
MethodPISA
2
C: Alcohol Dehydrogenases
F: Alcohol Dehydrogenases
G: Alcohol Dehydrogenases
H: Alcohol Dehydrogenases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,26417
Polymers101,0434
Non-polymers3,22113
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19410 Å2
ΔGint-263 kcal/mol
Surface area28490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.671, 238.522, 68.921
Angle α, β, γ (deg.)90.000, 113.350, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Alcohol Dehydrogenases


Mass: 25260.756 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leifsonia antarctica (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 984 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium acetate/Acetic acid, pH 7.0, 0.2M Zinc acetate, 20% PEG 1000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 219460 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 15.7
Reflection shellResolution: 1.58→1.61 Å / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 11079

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
MrBUMPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.58→49.56 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 11012 5 %RANDOM
Rwork0.1641 ---
obs0.1657 208376 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.67 Å2 / Biso mean: 10.53 Å2 / Biso min: 1.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å2-0 Å2-0.16 Å2
2---0.72 Å2-0 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 1.58→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13872 0 397 984 15253
Biso mean--11.85 17.66 -
Num. residues----2008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01314552
X-RAY DIFFRACTIONr_bond_other_d0.0370.01713391
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.62319916
X-RAY DIFFRACTIONr_angle_other_deg2.3871.56430725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95452008
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70623.723548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.607151824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7841548
X-RAY DIFFRACTIONr_chiral_restr0.0710.22024
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217032
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022864
X-RAY DIFFRACTIONr_rigid_bond_restr3.541327943
LS refinement shellResolution: 1.581→1.622 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 863 -
Rwork0.178 15093 -
all-15956 -
obs--97.95 %

+
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