[English] 日本語
Yorodumi
- PDB-7yav: Crystal structure of Diels-Alderase MaDA1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yav
TitleCrystal structure of Diels-Alderase MaDA1
ComponentsMaDA1
KeywordsPLANT PROTEIN / natural product biosynthetic enzyme
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesMorus alba (white mulberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLei, X.G. / Chen, R.C. / Du, X.X. / Yang, J. / Fan, J.P. / Guo, N.X. / Ding, Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22193073 China
National Natural Science Foundation of China (NSFC)91853202 China
CitationJournal: Nat Commun / Year: 2024
Title: The evolutionary origin of naturally occurring intermolecular Diels-Alderases from Morus alba.
Authors: Ding, Q. / Guo, N. / Gao, L. / McKee, M. / Wu, D. / Yang, J. / Fan, J. / Weng, J.K. / Lei, X.
History
DepositionJun 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: MaDA1
A: MaDA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,5457
Polymers122,3102
Non-polymers2,2355
Water10,178565
1
B: MaDA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1623
Polymers61,1551
Non-polymers1,0072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MaDA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3834
Polymers61,1551
Non-polymers1,2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.783, 104.521, 141.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein MaDA1


Mass: 61155.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Morus alba (white mulberry) / Production host: Trichoplusia ni (cabbage looper)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris (pH 5.5) and 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 71677 / % possible obs: 99.8 % / Redundancy: 12.7 % / CC1/2: 0.993 / CC star: 0.998 / Net I/σ(I): 4.7
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 3567 / CC1/2: 0.863 / CC star: 0.963

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootcoot 0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7E2V

7e2v


Resolution: 2.1→20 Å / SU ML: 0.2069 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.438
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2262 1999 2.89 %
Rwork0.1951 67263 -
obs0.196 69262 96.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.73 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8011 0 148 565 8724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00768371
X-RAY DIFFRACTIONf_angle_d0.848811367
X-RAY DIFFRACTIONf_chiral_restr0.05661232
X-RAY DIFFRACTIONf_plane_restr0.00751435
X-RAY DIFFRACTIONf_dihedral_angle_d13.29863023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.24171170.18873915X-RAY DIFFRACTION79.51
2.16-2.220.22841270.18534307X-RAY DIFFRACTION87.85
2.22-2.280.23831340.20294492X-RAY DIFFRACTION91.37
2.28-2.350.26161380.19114642X-RAY DIFFRACTION94.32
2.35-2.440.25581450.194884X-RAY DIFFRACTION98.47
2.44-2.540.2441450.18284886X-RAY DIFFRACTION99.51
2.54-2.650.21631470.18854924X-RAY DIFFRACTION99.67
2.65-2.790.26021470.18394938X-RAY DIFFRACTION99.88
2.79-2.960.22661470.18614978X-RAY DIFFRACTION99.82
2.96-3.190.20361490.18614971X-RAY DIFFRACTION100
3.19-3.510.21051490.19045001X-RAY DIFFRACTION100
3.51-4.020.20741490.1875017X-RAY DIFFRACTION100
4.02-5.050.19781500.18815047X-RAY DIFFRACTION100
5.05-200.25651550.24075261X-RAY DIFFRACTION99.94

+
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