[English] 日本語
Yorodumi
- PDB-8a2n: Structure of crocagin biosynthetic protein CgnD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a2n
TitleStructure of crocagin biosynthetic protein CgnD
ComponentsCgnD
KeywordsHYDROLASE / crocagin / RiPP / Protease
Function / homologySGNH hydrolase superfamily / hydrolase activity, acting on ester bonds / SGNH/GDSL hydrolase family protein
Function and homology information
Biological speciesChondromyces crocatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsAdam, S. / Koehnke, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KO 4116/3-2 Germany
CitationJournal: Nat.Chem. / Year: 2023
Title: Unusual peptide-binding proteins guide pyrroloindoline alkaloid formation in crocagin biosynthesis.
Authors: Adam, S. / Zheng, D. / Klein, A. / Volz, C. / Mullen, W. / Shirran, S.L. / Smith, B.O. / Kalinina, O.V. / Muller, R. / Koehnke, J.
History
DepositionJun 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation_author / Item: _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: CgnD
A: CgnD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3734
Polymers78,1812
Non-polymers1922
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.480, 102.060, 150.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein CgnD


Mass: 39090.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein underwent reductive lysine methylation prior to crystallization.
Source: (gene. exp.) Chondromyces crocatus (bacteria) / Gene: CMC5_025550 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0K1EC25
#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.: 251 / 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 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM ammonium sulfate, 100 mM MES pH 6.5 and 30% PEG 5000MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97833 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97833 Å / Relative weight: 1
ReflectionResolution: 2.35→39.56 Å / Num. obs: 30717 / % possible obs: 99.8 % / Redundancy: 12.6 % / Biso Wilson estimate: 28.42 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 21.2
Reflection shellResolution: 2.35→2.41 Å / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 8 / Num. unique obs: 2158 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
SCALAdata scaling
PHENIXAutosolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→39.56 Å / SU ML: 0.2177 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 19.677
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2237 1576 5.14 %
Rwork0.1715 29082 -
obs0.1742 30658 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.07 Å2
Refinement stepCycle: LAST / Resolution: 2.35→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4820 0 10 251 5081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01454956
X-RAY DIFFRACTIONf_angle_d1.53146705
X-RAY DIFFRACTIONf_chiral_restr0.0724728
X-RAY DIFFRACTIONf_plane_restr0.0122845
X-RAY DIFFRACTIONf_dihedral_angle_d14.719772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.430.26771290.18732558X-RAY DIFFRACTION98.17
2.43-2.510.24571510.17662565X-RAY DIFFRACTION99.63
2.51-2.610.25981350.17252630X-RAY DIFFRACTION99.78
2.61-2.730.2691370.1772634X-RAY DIFFRACTION99.96
2.73-2.880.23471410.17882602X-RAY DIFFRACTION99.96
2.88-3.060.20941230.18522628X-RAY DIFFRACTION99.96
3.06-3.290.26471660.17742636X-RAY DIFFRACTION100
3.29-3.620.21511230.1642663X-RAY DIFFRACTION99.93
3.62-4.150.1681430.14952663X-RAY DIFFRACTION100
4.15-5.220.18721740.1492673X-RAY DIFFRACTION99.96
5.22-39.560.24721540.19792830X-RAY DIFFRACTION99.8
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)
11.11459550499-0.273375947741-0.3109108857761.19766972069-0.543475759390.7775855230020.086957639846-0.1019690063490.418115329201-0.394463541114-0.07564558393270.0710495360452-0.610911737204-0.01957673155620.08882100513360.2958988846850.009769714120260.02021308186860.206770806421-0.05793027723180.342886848189102.260503416131.724574381177.66988451
22.250956341720.5570011593230.2076195454863.037182433020.1220408743222.6476013963-0.0476457935662-0.164681529469-0.1344200705690.1929542992910.0843213996689-0.3433758824150.2640470609820.40471814338-0.01393622740730.1566207290130.0695389628173-0.00489558641740.262801357713-0.01729499849580.14509198308106.484864397113.837988057184.271266492
31.00686467591-0.528880748211-0.05546097869750.9746340089340.386212365921.510245589540.07303977716970.0504942627063-0.0184713341693-0.113375094032-0.06738829552740.09256358719030.124011611891-0.257769082690.03556645894890.2376737360570.01705503257890.01877988846370.2420380755620.001249096732420.26006478258886.7534893334113.51679123175.258031476
42.412731571342.917617109721.262828794614.68515665412.6740128511.86115128109-0.3779191003890.1665158867920.648830800242-0.7262689957620.0245743324780.555592500486-0.731593773066-0.3974731505810.3434763128920.3574781639580.0438554679331-0.010450098410.331617218989-0.001750330209850.4415401451385.0396903238132.705442458183.439471044
52.512006118170.6339017478870.6345550768012.655716647380.159952379651.67715057616-0.0482636433661-0.374344085677-0.01290969489790.112901987038-0.01186983342-0.03991700752770.13987875023-0.2373995866970.06866936654320.191181138424-0.01203910322240.03824705054970.267648309324-0.02784323202090.14154331286388.3994325819117.280360418190.871285455
61.553844028-0.8452305339210.3031219847342.612144922831.046909760522.905467093980.05018027874880.145666822972-0.2023560544220.0313654808808-0.2111018600390.3598672686070.299330731037-0.4974434302510.06809707026670.136362122214-0.05007781822940.02855025837090.210905691277-0.05295094461970.18684569161490.765340627997.3010927465152.700223612
71.683694237931.04487670069-0.5889264040762.245403888270.6987096527492.347376873830.02279243501370.04678507178650.1120219179170.05187121336820.133203179854-0.159922043442-0.03839192272740.169898390141-0.1521526247790.2000787140250.07124166612630.02530152779030.212570303678-0.04343251479330.255951665176108.246170999105.165927428161.816757637
81.33602680786-0.06829615872250.5110424959691.774198696580.8396358957223.480530194280.003893621344250.168669201965-0.1790814247960.0794529395630.138664721139-0.2454816590020.1969561000550.377644276577-0.1683391795410.2167962935040.06753638724790.01541902706740.239112902065-0.06696567987830.274554748002108.94638030391.2240075981148.898249689
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1 through 34 )BA1 - 341 - 34
22chain 'B' and (resid 35 through 140 )BA35 - 14035 - 140
33chain 'B' and (resid 141 through 256 )BA141 - 256141 - 219
44chain 'B' and (resid 257 through 283 )BA257 - 283220 - 237
55chain 'B' and (resid 284 through 347 )BA284 - 347238 - 301
66chain 'A' and (resid 7 through 128 )AB7 - 1281 - 124
77chain 'A' and (resid 129 through 236 )AB129 - 236125 - 199
88chain 'A' and (resid 237 through 347 )AB237 - 347200 - 301

+
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://pdbjlvh1.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