[English] 日本語
Yorodumi
- PDB-6ljh: Crystal structure of Alcohol dehydrogenase 1 from Artemisia annua... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ljh
TitleCrystal structure of Alcohol dehydrogenase 1 from Artemisia annua in complex with NAD+
ComponentsAlcohol dehydrogenase 1
KeywordsOXIDOREDUCTASE / Sesquiterpene biosynthesis / dehydrogenase / zinc ion binding
Function / homology
Function and homology information


S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / formaldehyde catabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / zinc ion binding / nucleus / cytosol
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase 1
Similarity search - Component
Biological speciesArtemisia annua (sweet wormwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFeng, X. / Fan, S. / Li, M. / Zou, S. / Lv, G. / Wu, G. / Jin, Y. / Yang, Z.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0901800 China
National Natural Science Foundation of China (NSFC)8161101360 China
National Natural Science Foundation of China (NSFC)81872782 China
CitationJournal: To Be Published
Title: Crystal structure of Alcohol dehydrogenase 1 from Artemisia annua in complex with NAD+
Authors: Yang, Z.
History
DepositionDec 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: Alcohol dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,78812
Polymers41,5331
Non-polymers1,25511
Water7,927440
1
A: Alcohol dehydrogenase 1
hetero molecules

A: Alcohol dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,57524
Polymers83,0662
Non-polymers2,50922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8820 Å2
ΔGint-158 kcal/mol
Surface area28390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.446, 54.153, 90.374
Angle α, β, γ (deg.)90.000, 101.280, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Alcohol dehydrogenase 1 / Artemisinic aldehyde synthase


Mass: 41532.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Artemisia annua (sweet wormwood) / Gene: ADH1, CTI12_AA090660 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2U1Q018, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor

-
Non-polymers , 5 types, 451 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS MG256496 FOR THE PROTEIN. In MG256496, LEU(19th) ...AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS MG256496 FOR THE PROTEIN. In MG256496, LEU(19th) is SEL, GLY(20th) is SEL and VAL(78th) is ILE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 289.15 K / Method: evaporation / Details: PEG 10000, MES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 41073 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 17.92 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.033 / Rrim(I) all: 0.083 / Χ2: 0.928 / Net I/σ(I): 22.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 4111 / CC1/2: 0.931 / Rpim(I) all: 0.174 / Rrim(I) all: 0.432 / Χ2: 1.002 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DL9

4dl9


Resolution: 1.8→24.54 Å / SU ML: 0.1401 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.3676 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1798 1951 4.84 %
Rwork0.1517 38331 -
obs0.153 40282 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.87 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2907 0 0 440 3347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713001
X-RAY DIFFRACTIONf_angle_d0.9484078
X-RAY DIFFRACTIONf_chiral_restr0.0582471
X-RAY DIFFRACTIONf_plane_restr0.0051511
X-RAY DIFFRACTIONf_dihedral_angle_d5.41072429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.22461180.18522341X-RAY DIFFRACTION84.01
1.85-1.90.22091270.17942525X-RAY DIFFRACTION90.51
1.9-1.950.2331380.17852690X-RAY DIFFRACTION94.71
1.95-2.020.21711350.16452703X-RAY DIFFRACTION95.91
2.02-2.090.21821400.15512742X-RAY DIFFRACTION97.56
2.09-2.170.17241410.15072774X-RAY DIFFRACTION98.31
2.17-2.270.17641410.14812769X-RAY DIFFRACTION98.51
2.27-2.390.20651400.15272758X-RAY DIFFRACTION98.87
2.39-2.540.19791440.15032790X-RAY DIFFRACTION99.42
2.54-2.730.17481440.15642829X-RAY DIFFRACTION99.43
2.73-3.010.18311430.16052828X-RAY DIFFRACTION99.43
3.01-3.440.16871450.14822814X-RAY DIFFRACTION99.8
3.44-4.330.16481450.13392856X-RAY DIFFRACTION99.97
4.33-24.540.14741500.14732912X-RAY DIFFRACTION99.45

+
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