[English] 日本語
Yorodumi
- PDB-7cbf: Crystal structure of benzophenone synthase from Garcinia mangosta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cbf
TitleCrystal structure of benzophenone synthase from Garcinia mangostana L. pericarps reveals basis for substrate specificity and catalysis
Components2,4,6-trihydroxybenzophenone synthase
KeywordsTRANSFERASE / ACYLTRANSFERASE / BENZOPHENONE SYNTHASE / POLYKETIDE SYNTHASE / GmBPS
Function / homology
Function and homology information


2,4,6-trihydroxybenzophenone synthase / tetrahydroxybenzophenone synthase activity / trihydroxybenzophenone synthase activity / benzoyl-CoA metabolic process / malonyl-CoA metabolic process / polyketide biosynthetic process / acyltransferase activity
Similarity search - Function
Chalcone/stilbene synthase, N-terminal / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / IODIDE ION / 2,4,6-trihydroxybenzophenone synthase
Similarity search - Component
Biological speciesGarcinia mangostana (mangosteen)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsSongsiriritthigul, C. / Nualkaew, N. / Chen, C.-J.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of benzophenone synthase from Garcinia mangostana L. pericarps reveals basis for substrate specificity and catalysis.
Authors: Songsiriritthigul, C. / Nualkaew, N. / Ketudat-Cairnsb, J. / Chen, C.-J.
#1: Journal: Phytochemistry / Year: 2012
Title: Benzophenone synthase from Garcinia mangostana L. pericarps
Authors: Nualkaew, N. / Morita, H. / Shimokawa, Y. / Kinjo, K. / Kushiro, T. / De-Eknamkul, W. / Ebizuka, Y. / Abe, I.
History
DepositionJun 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2,4,6-trihydroxybenzophenone synthase
B: 2,4,6-trihydroxybenzophenone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,86618
Polymers88,0902
Non-polymers1,77616
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-16 kcal/mol
Surface area26380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.810, 98.330, 112.024
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 2,4,6-trihydroxybenzophenone synthase / GmBPS


Mass: 44045.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Garcinia mangostana (mangosteen) / Gene: BPS / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS
References: UniProt: L7NCQ3, 2,4,6-trihydroxybenzophenone synthase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.1 % / Description: rectangular morphology
Crystal growTemperature: 291 K / Method: batch mode / pH: 6.2 / Details: 20% (w/v) PEG 3,350, 0.2 M ammonium iodide, pH 6.2

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2015
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 35272 / % possible obs: 99.5 % / Redundancy: 2.4 % / Biso Wilson estimate: 17.52 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 9.67
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.14 / Num. unique obs: 6660 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CGK

1cgk


Resolution: 2.301→24.347 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.648 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.218
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2152 1763 5.004 %
Rwork0.1697 33467 -
all0.172 --
obs-35230 99.452 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.241 Å2
Baniso -1Baniso -2Baniso -3
1--0.567 Å2-0 Å2-0 Å2
2---0.124 Å20 Å2
3---0.691 Å2
Refinement stepCycle: LAST / Resolution: 2.301→24.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5838 0 44 317 6199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136009
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175665
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.6388127
X-RAY DIFFRACTIONr_angle_other_deg1.3111.57213159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.275766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24423.077286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.829151035
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5531530
X-RAY DIFFRACTIONr_chiral_restr0.0710.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026747
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021207
X-RAY DIFFRACTIONr_nbd_refined0.2060.21263
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.25334
X-RAY DIFFRACTIONr_nbtor_refined0.1550.22880
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22511
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2322
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1510.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.219
X-RAY DIFFRACTIONr_nbd_other0.1890.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.223
X-RAY DIFFRACTIONr_mcbond_it1.1221.5893049
X-RAY DIFFRACTIONr_mcbond_other1.1191.5873048
X-RAY DIFFRACTIONr_mcangle_it1.9092.3753811
X-RAY DIFFRACTIONr_mcangle_other1.912.3763812
X-RAY DIFFRACTIONr_scbond_it1.5261.8422960
X-RAY DIFFRACTIONr_scbond_other1.5251.8432961
X-RAY DIFFRACTIONr_scangle_it2.5472.664313
X-RAY DIFFRACTIONr_scangle_other2.5472.6614314
X-RAY DIFFRACTIONr_lrange_it4.14419.1446660
X-RAY DIFFRACTIONr_lrange_other4.05119.0876613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.301-2.3610.2581380.1982396X-RAY DIFFRACTION97.4615
2.361-2.4250.2241040.192391X-RAY DIFFRACTION99.9599
2.425-2.4960.251330.1752310X-RAY DIFFRACTION100
2.496-2.5720.2631270.1792258X-RAY DIFFRACTION99.8744
2.572-2.6570.2651220.1842174X-RAY DIFFRACTION99.9565
2.657-2.750.2441190.1762121X-RAY DIFFRACTION99.9554
2.75-2.8530.2161020.1682034X-RAY DIFFRACTION99.8597
2.853-2.970.238810.1632008X-RAY DIFFRACTION99.8566
2.97-3.1010.2151220.1591878X-RAY DIFFRACTION99.9001
3.101-3.2530.195920.1451815X-RAY DIFFRACTION99.8429
3.253-3.4280.188840.1511736X-RAY DIFFRACTION99.8902
3.428-3.6360.181940.1571641X-RAY DIFFRACTION99.77
3.636-3.8860.193850.1531547X-RAY DIFFRACTION99.7555
3.886-4.1960.216640.1551458X-RAY DIFFRACTION99.6726
4.196-4.5950.153730.1541320X-RAY DIFFRACTION99.1459
4.595-5.1350.209720.161211X-RAY DIFFRACTION98.5407
5.135-5.9250.191550.1971085X-RAY DIFFRACTION99.6503
5.925-7.2450.284460.208928X-RAY DIFFRACTION99.4893
7.245-10.1970.193320.167752X-RAY DIFFRACTION99.2405
10.197-24.340.254180.284402X-RAY DIFFRACTION89.7436

+
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