[English] 日本語
Yorodumi
- PDB-3ov3: G211F mutant of curcumin synthase 1 from Curcuma longa -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ov3
TitleG211F mutant of curcumin synthase 1 from Curcuma longa
ComponentsCurcumin synthase
KeywordsTRANSFERASE / type III polyketide synthase
Function / homology
Function and homology information


curcumin synthase / curcumin synthase activity / flavonoid biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Chalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Curcumin synthase 1
Similarity search - Component
Biological speciesCurcuma longa (turmeric)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKatsuyama, Y. / Miyazono, K. / Tanokura, M. / Ohnishi, Y. / Horinouchi, S.
CitationJournal: To be Published
Title: A hydrophobic cavity discovered in a curcumin synthase facilitates utilization of a beta-keto acid as an extender substrate for the atypical type III polyleteide synthase
Authors: Katsuyama, Y. / Miyazono, K. / Tanokura, M. / Ohnishi, Y. / Horinouchi, S.
History
DepositionSep 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Curcumin synthase
B: Curcumin synthase
C: Curcumin synthase
D: Curcumin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,93714
Polymers174,9164
Non-polymers1,02010
Water4,756264
1
A: Curcumin synthase
B: Curcumin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9687
Polymers87,4582
Non-polymers5105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-15 kcal/mol
Surface area28250 Å2
MethodPISA
2
C: Curcumin synthase
D: Curcumin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9687
Polymers87,4582
Non-polymers5105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-16 kcal/mol
Surface area28550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.700, 116.360, 221.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Curcumin synthase


Mass: 43729.109 Da / Num. of mol.: 4 / Mutation: G211F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Curcuma longa (turmeric) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: C0SVZ6
#2: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.3 M sodium malonate pH 7.0, 25% PEG3350 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 68101 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 44.365 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 13.81
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.5-2.560.7380.8332.436096505149430.89697.9
2.56-2.640.6150.692.935788496148620.74298
2.64-2.710.5080.5983.534870476646810.64298.2
2.71-2.80.4550.5353.934184466345770.57498.2
2.8-2.890.3640.4384.733412452244450.47198.3
2.89-2.990.3020.3645.632526439443210.39198.3
2.99-3.10.2530.3066.631580424941850.32898.5
3.1-3.230.1780.222930276408440210.23898.5
3.23-3.370.1360.17111.628995391538540.18398.4
3.37-3.540.1040.13314.227782376137140.14398.8
3.54-3.730.0780.10318.126445358035300.11198.6
3.73-3.950.0590.08222.424972340033510.08898.6
3.95-4.230.0490.06825.523412320331680.07498.9
4.23-4.560.0380.05730.121503296729310.06298.8
4.56-50.0370.05531.220144277927420.05998.7
5-5.590.0440.06227.318170251124830.06698.9
5.59-6.450.0480.06725.116063223822130.07298.9
6.45-7.910.0340.04931.513555191418940.05399
7.91-11.180.020.03343.910328150314830.03698.7
11.180.0190.0345.845528947030.03278.6

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.9 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 1 / SU B: 20.022 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 3451 5.1 %RANDOM
Rwork0.1918 ---
obs0.1946 68101 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 94.37 Å2 / Biso mean: 37.4472 Å2 / Biso min: 14.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--0.13 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12160 0 70 264 12494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02212482
X-RAY DIFFRACTIONr_angle_refined_deg1.451.96416878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1751552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38423.31565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.843152127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.56915104
X-RAY DIFFRACTIONr_chiral_restr0.0930.21847
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219524
X-RAY DIFFRACTIONr_mcbond_it0.5921.57724
X-RAY DIFFRACTIONr_mcangle_it1.131212372
X-RAY DIFFRACTIONr_scbond_it1.94934758
X-RAY DIFFRACTIONr_scangle_it3.2784.54506
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 248 -
Rwork0.244 4622 -
all-4870 -
obs--97.81 %
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)
10.68320.00470.1590.8822-0.14330.6547-0.03560.0358-0.04560.07050.06260.03170.0191-0.0607-0.0270.013-0.00390.01770.09820.00140.068819.3553-18.1807-52.636
20.6231-0.35050.28581.4868-0.46180.7251-0.2016-0.09030.04420.38330.1442-0.1426-0.0786-0.04550.05740.1410.0688-0.04440.0599-0.02650.024838.512-26.3327-29.8971
30.74830.02580.01890.7319-0.1380.89290.04460.04190.01330.0318-0.02970.0485-0.0995-0.036-0.01490.01760.01120.01950.0645-0.00060.093311.641823.2357-23.0217
40.95320.41820.16761.08660.0931.1850.0862-0.0021-0.05990.2709-0.0435-0.03550.12550.0406-0.04280.0789-0.001-0.0060.03390.01410.040317.04112.4849-0.8329
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 391
2X-RAY DIFFRACTION2B3 - 391
3X-RAY DIFFRACTION3C3 - 393
4X-RAY DIFFRACTION4D3 - 391

+
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://pdbjlvh1.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