[English] 日本語
Yorodumi
- PDB-7sml: Crystal Structure of L-GALACTONO-1,4-LACTONE DEHYDROGENASE de Myr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7sml
TitleCrystal Structure of L-GALACTONO-1,4-LACTONE DEHYDROGENASE de Myrciaria dubia
ComponentsL-GALACTONO-1,4-LACTONE DEHYDROGENASE
KeywordsPLANT PROTEIN / L-GALACTONO-1 / 4-LACTONE DEHYDROGENASE / Enzyme
Biological speciesMyrciaria dubia (camu-camu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSantillan, J.A.V. / Cabrejos, D.A.L. / Pereira, H.M. / Gomez, J.C.C. / Garratt, R.C.
Funding support Peru, 2items
OrganizationGrant numberCountry
Other government188-2018-INIA-PNIA-PASANTIA
Other government069-2019-FONDECYT Peru
CitationJournal: J.Exp.Bot. / Year: 2024
Title: Structural insights into the Smirnoff-Wheeler pathway for vitamin C production in the Amazon fruit Camu-Camu.
Authors: Vargas, J.A. / Sculaccio, S.A. / Pinto, A.P.A. / Pereira, H.D. / Mendes, L.F.S. / Flores, J.F. / Cobos, M. / Castro, J.C. / Garratt, R.C. / Leonardo, D.A.
History
DepositionOct 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-GALACTONO-1,4-LACTONE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)61,5691
Polymers61,5691
Non-polymers00
Water2,594144
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)64.157, 79.089, 89.939
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein L-GALACTONO-1,4-LACTONE DEHYDROGENASE


Mass: 61568.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myrciaria dubia (camu-camu) / Plasmid: pET151_D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): DE3 / References: L-galactonolactone dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M SPG (succinic acid, sodium dihydrogen phosphate, and glycine in the molar ratios 2:7:7); pH 7.0 and 25 % w/v PEG 1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRUS / Beamline: MANACA / Wavelength: 1.32363 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.32363 Å / Relative weight: 1
ReflectionResolution: 2.1→44.97 Å / Num. obs: 27421 / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.225 / Net I/σ(I): 7.9
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 13.7 % / Rmerge(I) obs: 2.469 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ALPHAFOLD

Resolution: 2.1→43.58 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 1419 5.18 %
Rwork0.206 --
obs0.208 27376 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.35 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3651 0 0 145 3796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.32781460.2982540X-RAY DIFFRACTION100
2.18-2.260.29331470.26632546X-RAY DIFFRACTION100
2.26-2.370.26961490.25082551X-RAY DIFFRACTION100
2.37-2.490.30361530.24112545X-RAY DIFFRACTION100
2.49-2.650.25421330.22962571X-RAY DIFFRACTION100
2.65-2.850.27971450.21682573X-RAY DIFFRACTION100
2.85-3.140.25261410.21992592X-RAY DIFFRACTION100
3.14-3.590.23511320.19792620X-RAY DIFFRACTION100
3.59-4.520.22171360.1792635X-RAY DIFFRACTION100
4.52-43.580.20871370.18422784X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6851-1.46090.18472.1120.08710.96320.0638-0.0156-0.0918-0.2067-0.09280.2107-0.0765-0.0613-0.01480.31250.00370.02430.34860.01810.37521.35849.544628.0094
21.8872-0.00270.6311.42550.13591.25980.0235-0.19810.07170.1212-0.0308-0.1345-0.0138-0.00570.02240.20630.01840.01410.25210.01970.219843.459159.273835.5785
30.2968-0.6460.58861.302-1.28331.3064-0.1776-0.3986-0.08980.43040.20380.03160.11280.0461-0.08770.41160.06240.02940.37450.04230.283242.397657.417936.149
41.33710.10040.29251.71730.57891.8039-0.03310.13390.1457-0.3677-0.0287-0.0664-0.28860.05030.0430.33010.02540.03150.25860.03610.252239.710666.98420.1778
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 24 THROUGH 119 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 120 THROUGH 320 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 321 THROUGH 349 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 350 THROUGH 502 )

+
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