[English] 日本語
Yorodumi
- PDB-6k3g: Crystal structure of 10-Hydroxygeraniol Dehydrogenase from Cantha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6k3g
TitleCrystal structure of 10-Hydroxygeraniol Dehydrogenase from Cantharanthus roseus in complex with NADP+
Components10-hydroxygeraniol oxidoreductase
KeywordsOXIDOREDUCTASE / 10-Hydroxygeraniol / Medium chain dehydrogenase/reductase / Cantharanthus roseus / MIA biosynthesis
Function / homology
Function and homology information


8-hydroxygeraniol dehydrogenase / 8-hydroxygeraniol dehydrogenase activity / organic substance metabolic process / oxidoreductase activity / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 10-hydroxygeraniol oxidoreductase / 8-hydroxygeraniol dehydrogenase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsSandholu, A.S. / Sharmila, P.M. / Thulasiram, H.V. / Kulkarni, K.A.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial ResearchBSC0124 India
CitationJournal: Proteins / Year: 2020
Title: Structural studies on 10-hydroxygeraniol dehydrogenase: A novel linear substrate-specific dehydrogenase from Catharanthus roseus.
Authors: Sandholu, A.S. / Mujawar, S.P. / Ramakrishnan, K. / Thulasiram, H.V. / Kulkarni, K.
History
DepositionMay 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 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
B: 10-hydroxygeraniol oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8624
Polymers38,9881
Non-polymers8743
Water50428
1
B: 10-hydroxygeraniol oxidoreductase
hetero molecules

B: 10-hydroxygeraniol oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7258
Polymers77,9762
Non-polymers1,7486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+y,y,-z-1/31
Buried area5670 Å2
ΔGint-115 kcal/mol
Surface area26170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.180, 53.180, 252.773
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

-
Components

#1: Protein 10-hydroxygeraniol oxidoreductase / 10-Hydroxygeraniol Dehydrogenase


Mass: 38988.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Gene: 10HGO / Plasmid: pRSET / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A067YF90, UniProt: Q6V4H0*PLUS
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, PEG 6000, 2-Methyl-2,4-pentanediol, Sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.0393 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 12, 2018
RadiationMonochromator: Si(111) double-crystal fixed-exit / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0393 Å / Relative weight: 1
ReflectionResolution: 2.41→46.06 Å / Num. obs: 16295 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 39.965 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.075 / Rrim(I) all: 0.146 / Net I/σ(I): 10.9
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 7 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1645 / CC1/2: 0.919 / Rpim(I) all: 0.5 / Rrim(I) all: 0.99 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLM7.2.1data reduction
Aimless0.5.21data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YQD

1yqd


Resolution: 2.41→42.16 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / SU B: 25.341 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R: 0.408 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26611 849 5.2 %RANDOM
Rwork0.20713 ---
obs0.21017 15375 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.796 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.12 Å20 Å2
2--0.23 Å2-0 Å2
3----0.75 Å2
Refinement stepCycle: 1 / Resolution: 2.41→42.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2689 0 50 28 2767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132802
X-RAY DIFFRACTIONr_bond_other_d0.0110.0172632
X-RAY DIFFRACTIONr_angle_refined_deg21.6633810
X-RAY DIFFRACTIONr_angle_other_deg1.3481.5866114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2825355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87922.793111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.24715461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3321510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023081
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02554
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4912.191423
X-RAY DIFFRACTIONr_mcbond_other1.4892.191422
X-RAY DIFFRACTIONr_mcangle_it2.5693.2831777
X-RAY DIFFRACTIONr_mcangle_other2.5693.2841778
X-RAY DIFFRACTIONr_scbond_it1.3212.3891379
X-RAY DIFFRACTIONr_scbond_other1.3212.3881380
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2473.532034
X-RAY DIFFRACTIONr_long_range_B_refined5.75841.12811955
X-RAY DIFFRACTIONr_long_range_B_other5.75641.10911952
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.473 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 49 -
Rwork0.327 1110 -
obs--98.89 %
Refinement TLS params.Method: refined / Origin x: -3.4559 Å / Origin y: 1.3996 Å / Origin z: -20.5336 Å
111213212223313233
T0.1425 Å2-0.1394 Å2-0.0073 Å2-0.6147 Å20.0418 Å2--0.3911 Å2
L0.8296 °20.0508 °2-0.6194 °2-0.0375 °2-0.2224 °2--3.1389 °2
S-0.0806 Å °0.4358 Å °0.1476 Å °0.0488 Å °-0.0488 Å °0.0187 Å °0.0331 Å °0.0471 Å °0.1293 Å °

+
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