[English] 日本語
Yorodumi
- PDB-8zag: Crystal structure of SkABA3 from Shimazuella kribbensis in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zag
TitleCrystal structure of SkABA3 from Shimazuella kribbensis in complex with PPi
ComponentsSesquiterpene synthases
KeywordsLYASE / SkABA3 / Sesquiterpene synthases / PPi
Function / homologyPYROPHOSPHATE 2-
Function and homology information
Biological speciesShimazuella kribbensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLi, S.Y. / Li, H. / Yang, Y. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Molecular insights into a distinct class of terpenoid cyclases.
Authors: Li, S. / Huang, J.W. / Min, J. / Li, H. / Ning, M. / Zhou, S. / Yang, Y. / Chen, C.C. / Guo, R.T.
History
DepositionApr 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_initial_refinement_model / refine
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type / _refine.pdbx_starting_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sesquiterpene synthases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7955
Polymers47,5051
Non-polymers2904
Water6,738374
1
A: Sesquiterpene synthases
hetero molecules

A: Sesquiterpene synthases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,58910
Polymers95,0092
Non-polymers5808
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5560 Å2
ΔGint-61 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.249, 64.607, 70.955
Angle α, β, γ (deg.)90.00, 108.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-798-

HOH

21A-872-

HOH

-
Components

#1: Protein Sesquiterpene synthases


Mass: 47504.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shimazuella kribbensis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 1.97 Å3/Da / Density % sol: 37.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.55 M Sodium chloride, 0.1 M Bis-Tris 6.5, 23% w/v PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. obs: 48426 / % possible obs: 99.4 % / Redundancy: 4.6 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.013 / Rrim(I) all: 0.029 / Χ2: 0.666 / Net I/σ(I): 18.6 / Num. measured all: 222383
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.6-1.664.50.09748580.9930.9980.0510.110.48199.7
1.66-1.724.30.07348030.9950.9990.040.0840.48699.6
1.72-1.84.70.06148640.9970.9990.0320.0690.599.6
1.8-1.94.30.04647800.9980.9990.0250.0530.5499.5
1.9-2.024.70.03648390.99910.0190.0410.58899.5
2.02-2.174.80.0348670.99910.0150.0330.6699.6
2.17-2.394.80.02548240.99910.0120.0280.71899.4
2.39-2.744.60.02248560.99910.0120.0250.79599.3
2.74-3.444.40.02148780.99910.0110.0230.999.7
3.44-254.80.02448570.99810.0120.0270.95997.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ZAF

8zaf


Resolution: 1.6→23.28 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.842 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22388 2433 5 %RANDOM
Rwork0.18137 ---
obs0.18349 45993 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.777 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å2-0.88 Å2
2--0.94 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.6→23.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 12 374 3297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132981
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172733
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.6514035
X-RAY DIFFRACTIONr_angle_other_deg1.5431.5726308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15621.136176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48715520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9791527
X-RAY DIFFRACTIONr_chiral_restr0.0920.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023319
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02682
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_it1.831.6721425
X-RAY DIFFRACTIONr_mcbond_other1.8241.6691423
X-RAY DIFFRACTIONr_mcangle_it2.7362.4951776
X-RAY DIFFRACTIONr_mcangle_other2.7392.4951776
X-RAY DIFFRACTIONr_scbond_it2.4681.9321556
X-RAY DIFFRACTIONr_scbond_other2.4671.9331549
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7642.7912247
X-RAY DIFFRACTIONr_long_range_B_refined5.52520.9143698
X-RAY DIFFRACTIONr_long_range_B_other5.45420.3513610
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å
RfactorNum. reflection% reflection
Rfree0.29 150 -
Rwork0.246 3411 -
obs--99 %

+
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