[English] 日本語
Yorodumi
- PDB-6ecu: SeMet substituted StiD O-MT residues 976-1266 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ecu
TitleSeMet substituted StiD O-MT residues 976-1266
ComponentsStiD protein
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / secondary metabolite biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
: / Beta-ketoacyl synthase-like, N-terminal / Polyketide synthase, methyltransferase domain / Methyltransferase in polyketide synthase (PKS) enzymes. / Methyltransferase type 12 / Methyltransferase domain / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding ...: / Beta-ketoacyl synthase-like, N-terminal / Polyketide synthase, methyltransferase domain / Methyltransferase in polyketide synthase (PKS) enzymes. / Methyltransferase type 12 / Methyltransferase domain / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / StiD protein
Similarity search - Component
Biological speciesStigmatella aurantiaca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å
AuthorsSkiba, M.A. / Bivins, M.M. / Smith, J.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK042303 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA108874 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008353 United States
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Structural Basis of Polyketide Synthase O-Methylation.
Authors: Skiba, M.A. / Bivins, M.M. / Schultz, J.R. / Bernard, S.M. / Fiers, W.D. / Dan, Q. / Kulkarni, S. / Wipf, P. / Gerwick, W.H. / Sherman, D.H. / Aldrich, C.C. / Smith, J.L.
History
DepositionAug 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: StiD protein
B: StiD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3244
Polymers71,5552
Non-polymers7692
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-10 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.300, 52.400, 68.700
Angle α, β, γ (deg.)89.600, 88.300, 81.100
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein StiD protein


Mass: 35777.434 Da / Num. of mol.: 2 / Fragment: oxygen methyltransferase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stigmatella aurantiaca (bacteria) / Gene: stiD / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RJY3
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.92 Å3/Da / Density % sol: 35.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 27% PEG 4000, 0.77 M LiCl, 0.1 M Tris pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2015
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.96→41.29 Å / Num. obs: 36676 / % possible obs: 96.7 % / Redundancy: 3.484 % / Biso Wilson estimate: 38.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.078 / Χ2: 0.951 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.96-2.012.2740.8720.9423960.4871.1284.1
2.01-2.073.6660.7121.8226190.7080.83696.7
2.07-2.133.5990.5512.2825880.8140.64896.8
2.13-2.193.6080.4252.8624670.8820.49996.9
2.19-2.263.460.3453.5524640.9030.40996.9
2.26-2.343.390.2684.3223280.930.3297.4
2.34-2.433.4730.235.0322830.9490.27397.6
2.43-2.533.5910.1826.2422180.9650.21498
2.53-2.643.7380.1517.3820900.9780.17798
2.64-2.773.7060.119.3620520.9880.12998.2
2.77-2.923.6430.09610.8819220.9880.11298.5
2.92-3.13.5620.08312.1518040.9910.09898.4
3.1-3.313.30.0713.7617360.9920.08498.5
3.31-3.583.4660.05316.4215760.9960.06398.3
3.58-3.923.6330.04319.2114570.9970.05198.4
3.92-4.383.7290.03821.0213300.9970.04598.4
4.38-5.063.630.03521.4111740.9970.04298.5
5.06-6.23.3370.04720.189900.9950.05798.5
6.2-8.773.5760.04621.637650.9960.05599
8.77-41.293.8350.038244170.9980.04499

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.96→41.29 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.69
RfactorNum. reflection% reflection
Rfree0.227 1841 5.02 %
Rwork0.1785 --
obs0.181 36668 94.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.58 Å2 / Biso mean: 54.7056 Å2 / Biso min: 20.95 Å2
Refinement stepCycle: final / Resolution: 1.96→41.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 52 116 4592
Biso mean--54.27 50.96 -
Num. residues----553
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.96-1.98580.4687810.43731539162055
1.9858-2.0130.37341290.35612545267489
2.013-2.04180.32971540.30792571272595
2.0418-2.07220.3641310.29842600273196
2.0722-2.10460.32851570.28512699285695
2.1046-2.13910.34831330.27132620275395
2.1391-2.1760.27721370.25032590272796
2.176-2.21560.30511450.25082688283396
2.2156-2.25820.2941370.2362653279095
2.2582-2.30430.25491270.23482642276996
2.3043-2.35440.27991570.22222635279296
2.3544-2.40910.27621310.21332675280696
2.4091-2.46940.30241400.21032655279597
2.4694-2.53610.24231430.19312709285297
2.5361-2.61070.25271310.20162684281597
2.6107-2.6950.24181560.19192638279497
2.695-2.79130.25111430.19052655279897
2.7913-2.9030.2571320.18822731286397
2.903-3.03510.21941430.18972623276697
3.0351-3.19510.21651340.18062723285797
3.1951-3.39520.23011520.17462632278496
3.3952-3.65720.20561320.1542676280897
3.6572-4.02490.18821440.13822668281296
4.0249-4.60670.18431450.12812669281496
4.6067-5.80140.19351350.14462649278496
5.8014-41.2990.18981400.15712705284598
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)
17.1240.6351-2.38514.5431-2.19092.14360.18591.00690.6285-0.5457-0.03490.1724-1.1511-0.0418-0.17410.76830.0261-0.0570.42330.05290.350628.42661.99834.4745
22.85630.19440.12153.8431-5.53528.04460.07130.11260.26290.0267-0.0988-0.591-0.58770.38610.0930.3586-0.02270.03940.2863-0.04960.349534.500854.302535.8654
34.5468-1.1961-0.77573.7182-1.40317.21050.2130.62530.3092-1.0841-0.2729-0.066-0.54210.03970.07680.70550.02160.00560.261-0.04840.294630.823940.205924.5783
44.7644-0.7111-0.68424.6993-0.33276.42440.21830.3139-0.3924-0.9265-0.18691.1004-0.0808-0.8824-0.03060.40410.0021-0.16410.3395-0.06760.468818.722735.236732.2911
56.0007-4.3354-7.02023.77385.95669.40190.21740.1365-0.2797-0.5661-0.37790.7622-0.0902-0.55730.16490.2618-0.0026-0.11990.3325-0.03010.437424.196436.997340.424
64.9628-2.01520.13316.19792.87595.04780.29430.2470.1948-0.2331-0.39111.648-0.3582-1.0216-0.14540.22060.04650.05810.45080.0380.640213.307339.468745.0206
73.11050.0918-0.50386.0884-0.84243.38020.20750.51610.6152-0.12990.00190.3485-1.1482-0.4121-0.13870.55180.14690.07990.35710.03550.360922.521358.636638.9011
88.8329-0.84992.71923.1474-2.1832.3440.47782.0284-0.1435-0.3383-0.40880.424-0.84040.13520.30310.75250.38740.13650.77580.01370.566914.87660.646836.728
91.9297-1.57790.19948.0452-2.60084.6591-0.0472-0.2643-0.17290.31120.29690.511-0.3263-0.2136-0.22930.18190.04260.02450.2602-0.00080.278823.669638.765250.3942
101.87450.92460.78813.9736-1.96546.8280.1888-0.2894-0.10080.80340.07480.39350.4438-1.0356-0.16540.4678-0.00830.07540.4879-0.01390.346724.476619.95177.7765
116.55021.45661.24475.6429-1.50944.9160.3889-0.4132-0.6043-0.1207-0.3828-0.16461.49280.0316-0.04440.5943-0.03240.0720.295-0.01870.287632.41968.041962.0091
122.13910.0057-0.01525.3935-0.08113.24730.0008-0.1219-0.1205-0.0139-0.295-0.5660.37490.81690.25920.23630.0790.04340.46570.07990.317642.321522.371259.0744
131.33170.1756-0.95642.6835-1.97438.0250.0103-0.2185-0.06370.4548-0.1324-0.08670.0870.29460.12760.2481-0.0228-0.01810.272-0.03530.298434.376427.861369.9752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 980 through 1007 )A980 - 1007
2X-RAY DIFFRACTION2chain 'A' and (resid 1008 through 1028 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1029 through 1090 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1091 through 1128 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1129 through 1142 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1143 through 1170 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1171 through 1206 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 1207 through 1226 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 1227 through 1265 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 979 through 1028 )B979 - 1028
11X-RAY DIFFRACTION11chain 'B' and (resid 1029 through 1089 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 1090 through 1170 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 1171 through 1267 )B0

+
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