[English] 日本語
Yorodumi
- PDB-2rh8: Structure of apo anthocyanidin reductase from vitis vinifera -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rh8
TitleStructure of apo anthocyanidin reductase from vitis vinifera
ComponentsAnthocyanidin reductase
KeywordsOXIDOREDUCTASE / flavonoids / Rossmann fold / short chain dehydrogenase/reductase
Function / homology
Function and homology information


anthocyanidin reductase [(2S)-flavan-3-ol-forming] / anthocyanidin reductase activity / racemase and epimerase activity / flavonoid biosynthetic process / NADP binding
Similarity search - Function
: / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Anthocyanidin reductase ((2S)-flavan-3-ol-forming)
Similarity search - Component
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å
AuthorsGargouri, M. / Mauge, C. / Langlois D'Estaintot, B. / Granier, T. / Manigan, C. / Gallois, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure and epimerase activity of anthocyanidin reductase from Vitis vinifera.
Authors: Gargouri, M. / Manigand, C. / Mauge, C. / Granier, T. / Langlois d'Estaintot, B. / Cala, O. / Pianet, I. / Bathany, K. / Chaudiere, J. / Gallois, B.
History
DepositionOct 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Anthocyanidin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8402
Polymers36,8041
Non-polymers351
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.470, 50.470, 440.406
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-352-

HOH

-
Components

#1: Protein Anthocyanidin reductase


Mass: 36804.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis vinifera (wine grape) / Gene: VvANR / Plasmid: pETGB-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5FB34, EC: 1.3.1.77
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 293 K / pH: 7.5
Details: NH4 acetate 150 mM, PEG 3350, Hepes 100 mM, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 20, 2007 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.22→43.727 Å / Num. obs: 17253 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 42.07 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 5.6
Reflection shellResolution: 2.22→2.34 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2 / Rsym value: 0.343 / % possible all: 98.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C29

2c29


Resolution: 2.22→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.271 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.279 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 851 5 %RANDOM
Rwork0.199 ---
obs0.203 17114 95.7 %-
all-17114 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20.44 Å20 Å2
2--0.88 Å20 Å2
3----1.32 Å2
Refine analyzeLuzzati coordinate error obs: 0.277 Å
Refinement stepCycle: LAST / Resolution: 2.22→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2309 0 1 123 2433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222354
X-RAY DIFFRACTIONr_bond_other_d0.0010.021522
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.9663200
X-RAY DIFFRACTIONr_angle_other_deg1.22933761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7655309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82425.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54315379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.97154
X-RAY DIFFRACTIONr_chiral_restr0.1180.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022605
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02444
X-RAY DIFFRACTIONr_nbd_refined0.210.2499
X-RAY DIFFRACTIONr_nbd_other0.1840.21488
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21187
X-RAY DIFFRACTIONr_nbtor_other0.090.21224
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2127
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1750.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3450.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2131608
X-RAY DIFFRACTIONr_mcbond_other0.6953630
X-RAY DIFFRACTIONr_mcangle_it4.56562491
X-RAY DIFFRACTIONr_scbond_it4.3034870
X-RAY DIFFRACTIONr_scangle_it5.9158709
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.22→2.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 55 -
Rwork0.222 1189 -
obs--98.65 %

+
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