[English] 日本語
Yorodumi
- PDB-29mu: Sesterterpene Synthase from Streptomyces mobaraensis (Sestermobar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 29mu
TitleSesterterpene Synthase from Streptomyces mobaraensis (Sestermobaraene Synthase, SmTS1) in complex with pyrophosphate (PPi)
ComponentsGlutamate dehydrogenase/leucine dehydrogenase
KeywordsLYASE / Type I Terpene Synthases / Terpene Cyclization Mechanism / Carbocation Cascade / Enzyme Engineering / Active Site Mutagenesis / Chemodiversity
Function / homologyTerpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / PHOSPHATE ION / PYROPHOSPHATE 2- / Glutamate dehydrogenase/leucine dehydrogenase
Function and homology information
Biological speciesStreptomyces mobaraensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTroycke, P. / Li, H. / Yang, K. / Dickschat, J.S. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GR 1861/13-1 (project number 542938137) Germany
CitationJournal: to be published
Title: Modular Active-Site Architecture Directs Divergent Carbocation Cascades in Sesterterpene Synthases
Authors: Troycke, P. / Li, H. / Yang, K. / Dickschat, J.S. / Groll, M.
History
DepositionMar 23, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate dehydrogenase/leucine dehydrogenase
B: Glutamate dehydrogenase/leucine dehydrogenase
C: Glutamate dehydrogenase/leucine dehydrogenase
D: Glutamate dehydrogenase/leucine dehydrogenase
E: Glutamate dehydrogenase/leucine dehydrogenase
F: Glutamate dehydrogenase/leucine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,05019
Polymers241,0576
Non-polymers99313
Water1,49583
1
A: Glutamate dehydrogenase/leucine dehydrogenase
D: Glutamate dehydrogenase/leucine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8028
Polymers80,3522
Non-polymers4496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-49 kcal/mol
Surface area26200 Å2
MethodPISA
2
B: Glutamate dehydrogenase/leucine dehydrogenase
C: Glutamate dehydrogenase/leucine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6726
Polymers80,3522
Non-polymers3204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-35 kcal/mol
Surface area26820 Å2
MethodPISA
3
E: Glutamate dehydrogenase/leucine dehydrogenase
F: Glutamate dehydrogenase/leucine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5775
Polymers80,3522
Non-polymers2253
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-31 kcal/mol
Surface area26530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.440, 228.690, 63.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
Glutamate dehydrogenase/leucine dehydrogenase


Mass: 40176.184 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces mobaraensis (bacteria) / Gene: H340_07296 / Plasmid: pETDuet-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M3CB08
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM Tris, 0.15 M MgCl2, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 64377 / % possible obs: 97.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6403 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU B: 67.232 / SU ML: 0.481 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25194 3214 5 %RANDOM
Rwork0.22657 ---
obs0.22788 61073 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 98.543 Å2
Baniso -1Baniso -2Baniso -3
1--11.94 Å2-0 Å2-0 Å2
2---9.82 Å20 Å2
3---21.77 Å2
Refinement stepCycle: 1 / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16171 0 49 83 16303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01316693
X-RAY DIFFRACTIONr_bond_other_d0.0020.01415274
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.65322878
X-RAY DIFFRACTIONr_angle_other_deg1.0291.57235063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.49152035
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.30220.59949
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.159152432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.82615154
X-RAY DIFFRACTIONr_chiral_restr0.0340.22171
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0218935
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023985
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_it1.3667.8428170
X-RAY DIFFRACTIONr_mcbond_other1.3667.8418169
X-RAY DIFFRACTIONr_mcangle_it1.85111.74710195
X-RAY DIFFRACTIONr_mcangle_other1.85111.74810196
X-RAY DIFFRACTIONr_scbond_it1.0167.9858523
X-RAY DIFFRACTIONr_scbond_other1.0157.9788517
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.46711.91312677
X-RAY DIFFRACTIONr_long_range_B_refined5.21691.92718647
X-RAY DIFFRACTIONr_long_range_B_other5.13191.8618638
X-RAY DIFFRACTIONr_rigid_bond_restr0.736331961
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 237 -
Rwork0.425 4502 -
obs--98.73 %
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)
10.3968-0.16740.15441.027-0.16860.17790.02630.0001-0.2050.0172-0.0171-0.0517-0.0918-0.0002-0.00920.2928-0.018-0.01460.3812-0.0010.1551-71.529162.8621-37.9405
20.3250.39380.19730.96210.02640.30250.12630.0427-0.09310.04830.00270.21450.08040.1143-0.12890.3054-0.0114-0.02330.29820.01190.3247-43.153335.2855-18.5393
30.28240.1907-0.01651.61790.03250.01630.03940.00820.140.1438-0.02680.08810.05020.0511-0.01260.3677-0.01740.04720.422-0.01340.0719-28.365563.4167-13.5557
40.789-0.3571-0.00191.388-0.11640.03710.03880.12370.2519-0.0791-0.05090.02070.01280.0180.01210.3142-0.0248-0.02210.3510.06450.1152-84.59189.8666-50.3982
50.87790.33690.2240.66690.12590.26390.006-0.04280.1490.0255-0.0179-0.1540.0534-0.0520.01190.4056-0.04760.03860.3969-0.00380.1144-19.5672107.1381-14.1304
60.8890.05530.30170.413-0.13760.2983-0.08170.02730.2269-0.01790.03750.20040.0755-0.02910.04420.3039-0.07740.04390.37560.00710.1613-48.1063105.055-29.0273
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 349
2X-RAY DIFFRACTION2B14 - 349
3X-RAY DIFFRACTION3C14 - 350
4X-RAY DIFFRACTION4D16 - 348
5X-RAY DIFFRACTION5E14 - 350
6X-RAY DIFFRACTION6F16 - 349

+
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