[English] 日本語
Yorodumi
- PDB-6e6y: Dieckmann cyclase, NcmC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6e6y
TitleDieckmann cyclase, NcmC
ComponentsDieckmann cyclase, NcmC
KeywordsBIOSYNTHETIC PROTEIN / Dieckmann cyclase / off-loading / Dieckmann condensation
Function / homologyAlpha/Beta hydrolase fold / NcmC
Function and homology information
Biological speciesSaccharothrix syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsCogan, D.P. / Nair, S.K.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Structural Basis for Enzymatic Off-Loading of Hybrid Polyketides by Dieckmann Condensation.
Authors: Cogan, D.P. / Ly, J. / Nair, S.K.
History
DepositionJul 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 21, 2020Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _software.name
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dieckmann cyclase, NcmC
B: Dieckmann cyclase, NcmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8214
Polymers57,6292
Non-polymers1922
Water8,665481
1
A: Dieckmann cyclase, NcmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9102
Polymers28,8141
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dieckmann cyclase, NcmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9102
Polymers28,8141
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.435, 80.435, 77.923
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Dieckmann cyclase, NcmC


Mass: 28814.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharothrix syringae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1X9WEN9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.75 M ammonium sulfate, 1.9% (w/v) PEG 400, 0.1 M HEPES pH 7.0, 3 mM DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97858 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97858 Å / Relative weight: 1
ReflectionResolution: 1.6→80.43 Å / Num. obs: 64619 / % possible obs: 99 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.8
Reflection shellResolution: 1.6→1.657 Å / Rmerge(I) obs: 0.69 / Num. unique obs: 5773

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
autoPROCdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→80.43 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.603 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20396 3275 5.1 %RANDOM
Rwork0.16862 ---
obs0.17046 61355 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.263 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 1.6→80.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3966 0 10 481 4457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194055
X-RAY DIFFRACTIONr_bond_other_d0.0020.023810
X-RAY DIFFRACTIONr_angle_refined_deg2.0561.9675539
X-RAY DIFFRACTIONr_angle_other_deg1.10538729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8415533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89522.093172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20115572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0121546
X-RAY DIFFRACTIONr_chiral_restr0.1340.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214657
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02885
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_it2.0141.5882141
X-RAY DIFFRACTIONr_mcbond_other2.0121.5872140
X-RAY DIFFRACTIONr_mcangle_it3.0352.3722671
X-RAY DIFFRACTIONr_mcangle_other3.0352.3732672
X-RAY DIFFRACTIONr_scbond_it3.0881.9171914
X-RAY DIFFRACTIONr_scbond_other3.0841.9161911
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7212.7462863
X-RAY DIFFRACTIONr_long_range_B_refined6.93820.8924658
X-RAY DIFFRACTIONr_long_range_B_other6.81420.4094551
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 214 -
Rwork0.225 3896 -
obs--84.22 %

+
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