[English] 日本語
Yorodumi
- PDB-4mc3: Hedycaryol synthase in complex with Nerolidol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mc3
TitleHedycaryol synthase in complex with Nerolidol
ComponentsPutative sesquiterpene cyclase
KeywordsLYASE / cyclase / terpenoid / Terpene alpha domain class I / helix break / helix dipol / surrogate
Function / homology
Function and homology information


(2Z,6E)-hedycaryol synthase / terpene synthase activity / terpenoid biosynthetic process / metal ion binding
Similarity search - Function
Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(3R,6E)-3,7,11-trimethyldodeca-1,6,10-trien-3-ol / (2Z,6E)-hedycaryol synthase
Similarity search - Component
Biological speciesKitasatospora setae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBaer, P. / Rabe, P. / Cirton, C. / Oliveira Mann, C. / Kaufmann, N. / Groll, M. / Dickschat, J.
CitationJournal: Chembiochem / Year: 2014
Title: Hedycaryol synthase in complex with nerolidol reveals terpene cyclase mechanism.
Authors: Baer, P. / Rabe, P. / Citron, C.A. / de Oliveira Mann, C.C. / Kaufmann, N. / Groll, M. / Dickschat, J.S.
History
DepositionAug 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative sesquiterpene cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9242
Polymers38,7011
Non-polymers2221
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.440, 59.440, 182.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

-
Components

#1: Protein Putative sesquiterpene cyclase


Mass: 38701.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora setae (bacteria)
Strain: ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054
Gene: KSE_00200t, KSE_76540t / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: E4MYY0, Lyases; Carbon-oxygen lyases; Acting on phosphates
#2: Chemical ChemComp-28U / (3R,6E)-3,7,11-trimethyldodeca-1,6,10-trien-3-ol / trans-Nerolidol


Mass: 222.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4M Sodium formiate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2012
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→44.855 Å / Num. all: 62111 / Num. obs: 61118 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.4
Reflection shellResolution: 1.5→1.6 Å / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.6 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Hedycaryol Synthase experimentally phased with HgCl2

Resolution: 1.5→44.855 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.456 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18922 3006 5 %RANDOM
Rwork0.14324 ---
obs0.14549 57110 98.35 %-
all-60116 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.987 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.43 Å20 Å2
2--0.43 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 16 278 2561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192337
X-RAY DIFFRACTIONr_bond_other_d0.0020.022229
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.9533177
X-RAY DIFFRACTIONr_angle_other_deg1.08735081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3845283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46422.895114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91915363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1211524
X-RAY DIFFRACTIONr_chiral_restr0.1170.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212640
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02564
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.53534566
X-RAY DIFFRACTIONr_sphericity_free31.898589
X-RAY DIFFRACTIONr_sphericity_bonded11.88154701
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 208 -
Rwork0.252 3959 -
obs--95.62 %
Refinement TLS params.Method: refined / Origin x: 7.8158 Å / Origin y: 39.9741 Å / Origin z: 13.5961 Å
111213212223313233
T0.0119 Å2-0.0005 Å2-0.0116 Å2-0.0131 Å2-0.0005 Å2--0.0214 Å2
L0.2031 °2-0.2306 °20.2073 °2-0.3765 °20.0373 °2--0.8816 °2
S0.0128 Å °-0.0024 Å °0.0214 Å °-0.004 Å °0.0176 Å °-0.0544 Å °0.0032 Å °0.0153 Å °-0.0304 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