[English] 日本語
Yorodumi
- PDB-2iod: Binding of two substrate analogue molecules to dihydroflavonol-4-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2iod
TitleBinding of two substrate analogue molecules to dihydroflavonol-4-reductase alters the functional geometry of the catalytic site
ComponentsDihydroflavonol 4-reductaseDihydrokaempferol 4-reductase
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD
Function / homology
Function and homology information


dihydroflavonol 4-reductase / dihydrokaempferol 4-reductase activity / flavanone 4-reductase activity / flavanone 4-reductase / anthocyanin-containing compound biosynthetic process / flavonoid biosynthetic process / nucleotide 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
Chem-MYC / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydroflavonol 4-reductase / Flavanone 4-reductase
Similarity search - Component
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsPetit, P. / Langlois d'Estaintot, B. / Granier, T. / Gallois, B.
CitationJournal: To be Published
Title: Binding of two substrate analogue molecules to dihydroflavonol-4-reductase alters the functional geometry of the catalytic site
Authors: Petit, P. / Langlois d'Estaintot, B. / Granier, T. / Gallois, B.
History
DepositionOct 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Dihydroflavonol 4-reductase
B: Dihydroflavonol 4-reductase
C: Dihydroflavonol 4-reductase
D: Dihydroflavonol 4-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,29716
Polymers150,7774
Non-polymers5,52012
Water13,836768
1
A: Dihydroflavonol 4-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0744
Polymers37,6941
Non-polymers1,3803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydroflavonol 4-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0744
Polymers37,6941
Non-polymers1,3803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dihydroflavonol 4-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0744
Polymers37,6941
Non-polymers1,3803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dihydroflavonol 4-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0744
Polymers37,6941
Non-polymers1,3803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.231, 177.958, 92.597
Angle α, β, γ (deg.)90.000, 104.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUMETMETAA6 - 886 - 88
21GLUGLUMETMETBB6 - 886 - 88
31GLUGLUMETMETCC6 - 886 - 88
41GLUGLUMETMETDD6 - 886 - 88
52LYSLYSHISHISAA93 - 32993 - 329
62LYSLYSHISHISBB93 - 32993 - 329
72LYSLYSHISHISCC93 - 32993 - 329
82LYSLYSHISHISDD93 - 32993 - 329

-
Components

#1: Protein
Dihydroflavonol 4-reductase / Dihydrokaempferol 4-reductase


Mass: 37694.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis vinifera (wine grape) / Gene: dfr1 / Plasmid: PQE(30XA) / Production host: Escherichia coli (E. coli) / Strain (production host): M15(PREP4)
References: UniProt: P93799, UniProt: P51110*PLUS, dihydroflavonol 4-reductase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-MYC / 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE / 2-(3,4,5-TRIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-4H-1-BENZOPYRAN-4-ONE / 3,3',4',5,5',7-HEXAHYDROXYFLAVONE / MYRICETIN / CANNABISCETIN / Myricetin


Mass: 318.235 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H10O8
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 768 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 50mM NaCl, 29% PEG3350, 100mM Hepes, 3mM NaN3, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.04 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 19, 2005 / Details: MIRRORS
RadiationMonochromator: Si (311) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.06→89.535 Å / Num. obs: 89953 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 4
Reflection shellResolution: 2.06→2.17 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 2.1 / Num. measured all: 30567 / Num. unique all: 12398 / Rsym value: 0.505 / % possible all: 94.1

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ProDCdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2c29

2c29


Resolution: 2.06→89.44 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.918 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 4501 5 %RANDOM
Rwork0.189 ---
all0.193 ---
obs0.193 89894 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.307 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-0.85 Å2
2--2.1 Å20 Å2
3----2.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.261 Å
Refinement stepCycle: LAST / Resolution: 2.06→89.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9981 0 376 768 11125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210630
X-RAY DIFFRACTIONr_bond_other_d00.026899
X-RAY DIFFRACTIONr_angle_refined_deg1.9252.00114521
X-RAY DIFFRACTIONr_angle_other_deg4.316316893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8151297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87723.869398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.464151694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0341544
X-RAY DIFFRACTIONr_chiral_restr0.1040.21629
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211588
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022071
X-RAY DIFFRACTIONr_nbd_refined0.2110.22476
X-RAY DIFFRACTIONr_nbd_other0.2350.27042
X-RAY DIFFRACTIONr_nbtor_refined0.1870.25165
X-RAY DIFFRACTIONr_nbtor_other0.1130.24803
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2761
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0080.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1750.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.213
X-RAY DIFFRACTIONr_mcbond_it2.56836474
X-RAY DIFFRACTIONr_mcbond_other032599
X-RAY DIFFRACTIONr_mcangle_it3.877610471
X-RAY DIFFRACTIONr_scbond_it2.77834156
X-RAY DIFFRACTIONr_scangle_it3.82864048
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1889MEDIUM POSITIONAL0.230.5
2B1889MEDIUM POSITIONAL0.160.5
3C1889MEDIUM POSITIONAL0.160.5
4D1889MEDIUM POSITIONAL0.170.5
1A2188LOOSE POSITIONAL0.495
2B2188LOOSE POSITIONAL0.475
3C2188LOOSE POSITIONAL0.425
4D2188LOOSE POSITIONAL0.415
1A1889MEDIUM THERMAL2.022
2B1889MEDIUM THERMAL2.082
3C1889MEDIUM THERMAL1.752
4D1889MEDIUM THERMAL2.272
1A2188LOOSE THERMAL3.9910
2B2188LOOSE THERMAL3.8610
3C2188LOOSE THERMAL3.2710
4D2188LOOSE THERMAL4.310
LS refinement shellResolution: 2.06→2.114 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 294 -
Rwork0.299 5837 -
obs-6131 91.28 %

+
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