[English] 日本語
Yorodumi
- PDB-4tkt: Streptomyces platensis isomigrastatin ketosynthase domain MgsF KS6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tkt
TitleStreptomyces platensis isomigrastatin ketosynthase domain MgsF KS6
ComponentsAT-less polyketide synthase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / NatPro / Enzyme Discovery for Natural Product Biosynthesis
Function / homology
Function and homology information


: / S-adenosylmethionine-dependent methyltransferase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process
Similarity search - Function
Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #100 / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methyltransferase type 12 / Methyltransferase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain ...Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #100 / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methyltransferase type 12 / Methyltransferase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 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 / Phosphopantetheine attachment site. / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AT-less polyketide synthase
Similarity search - Component
Biological speciesStreptomyces platensis subsp. rosaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4289 Å
AuthorsChang, C. / Li, H. / Endres, M. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A. ...Chang, C. / Li, H. / Endres, M. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural and evolutionary relationships of "AT-less" type I polyketide synthase ketosynthases.
Authors: Lohman, J.R. / Ma, M. / Osipiuk, J. / Nocek, B. / Kim, Y. / Chang, C. / Cuff, M. / Mack, J. / Bigelow, L. / Li, H. / Endres, M. / Babnigg, G. / Joachimiak, A. / Phillips, G.N. / Shen, B.
History
DepositionMay 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Other
Revision 1.2Nov 2, 2016Group: Database references / Structure summary
Revision 1.3Mar 22, 2023Group: Database references / Derived calculations / Structure summary
Category: audit_author / database_2 / pdbx_struct_oper_list
Item: _audit_author.name / _database_2.pdbx_DOI ..._audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AT-less polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1877
Polymers66,5801
Non-polymers6076
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.331, 83.331, 203.725
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein AT-less polyketide synthase


Mass: 66580.242 Da / Num. of mol.: 1 / Fragment: UNP Residues 3137-3758
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces platensis subsp. rosaceus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: D0U2E4

-
Non-polymers , 5 types, 167 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6M Magnesium sulfate, 0.1M MES pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97913 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2014
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 2.4289→50 Å / Num. all: 31779 / Num. obs: 31725 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.079 / Χ2: 0.9 / Net I/av σ(I): 27.96 / Net I/σ(I): 8.2 / Num. measured all: 326286
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4289-2.47100.98315570.66100
2.47-2.5210.40.85515670.666100
2.52-2.5710.50.68915330.668100
2.57-2.6210.50.6815900.675100
2.62-2.6710.50.51215740.677100
2.67-2.7410.50.44515190.704100
2.74-2.8110.50.40616040.709100
2.81-2.8810.50.30215540.724100
2.88-2.9710.50.21815740.744100
2.97-3.0610.40.19115670.787100
3.06-3.1710.40.15315590.861100
3.17-3.310.40.11515870.941100
3.3-3.4510.40.115811.05799.9
3.45-3.6310.30.07915891.221100
3.63-3.8610.20.07215761.269100
3.86-4.1510.20.06416211.359100
4.15-4.5710.10.05915951.386100
4.57-5.23100.05216241.235100
5.23-6.59100.04416440.895100
6.59-509.50.03917100.7597

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 2.4289→41.612 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.23 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 1334 5.08 %Random selection
Rwork0.1827 ---
obs0.1854 26238 82.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4289→41.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4330 0 35 161 4526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034474
X-RAY DIFFRACTIONf_angle_d0.6556089
X-RAY DIFFRACTIONf_dihedral_angle_d10.6591560
X-RAY DIFFRACTIONf_chiral_restr0.025658
X-RAY DIFFRACTIONf_plane_restr0.003806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4289-2.51580.2589590.27521213X-RAY DIFFRACTION41
2.5158-2.61650.3862930.27251427X-RAY DIFFRACTION49
2.6165-2.73550.34511050.26751732X-RAY DIFFRACTION59
2.7355-2.87970.38771260.25772715X-RAY DIFFRACTION90
2.8797-3.06010.26531620.24012876X-RAY DIFFRACTION97
3.0601-3.29630.30331640.21652884X-RAY DIFFRACTION97
3.2963-3.62780.22551590.18132922X-RAY DIFFRACTION97
3.6278-4.15230.21011510.14672928X-RAY DIFFRACTION97
4.1523-5.22990.16881640.13433021X-RAY DIFFRACTION99
5.2299-41.6180.21311510.16873186X-RAY DIFFRACTION98
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)
11.1805-0.1779-0.18411.9741-0.07962.5781-0.0390.21890.3436-0.1189-0.01140.1197-0.6115-0.26650.08180.4037-0.0096-0.1040.2673-0.0250.322835.221520.062329.2082
21.51760.02350.30670.91760.20531.8246-0.09970.4120.0667-0.20470.0547-0.0386-0.19940.13740.04780.2759-0.0731-0.00980.37330.02970.226741.7726.362216.1749
32.0237-0.7904-0.74041.017-0.1862.1176-0.0841-0.0296-0.34320.04030.00980.1143-0.007-0.20820.07690.222-0.0370.00490.338-0.03290.361335.0536-0.549526.9845
40.8264-0.28290.20711.22080.18081.4346-0.2029-0.09660.07410.08360.15250.0211-0.1730.30490.0260.2088-0.0592-0.03210.29240.02320.26644.70769.58930.1947
51.0308-0.0154-0.71121.18290.06110.6429-0.0745-0.07210.3160.04490.0893-0.2342-0.48360.45070.0130.3579-0.1751-0.07180.5367-0.02860.400855.043217.6840.7344
60.8687-0.41980.04511.730.02160.7726-0.1514-0.0670.5217-0.07350.0386-0.4026-0.77510.49250.08740.5521-0.228-0.05290.44680.01470.561752.149227.033734.6031
70.0709-0.0596-0.18590.0147-0.25882.1618-0.0580.02390.2291-0.1359-0.0614-0.1002-0.28330.06290.12670.4745-0.16620.06630.5150.04510.40751.523717.26024.335
80.28650.104-0.190.6075-0.44312.1425-0.04020.07020.0571-0.26150.0067-0.165-0.02930.4150.01290.4058-0.06840.04980.55440.04130.35848.385311.2928-2.3169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3139 through 3199 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3200 through 3257 )
3X-RAY DIFFRACTION3chain 'A' and (resid 3258 through 3295 )
4X-RAY DIFFRACTION4chain 'A' and (resid 3296 through 3400 )
5X-RAY DIFFRACTION5chain 'A' and (resid 3401 through 3476 )
6X-RAY DIFFRACTION6chain 'A' and (resid 3477 through 3565 )
7X-RAY DIFFRACTION7chain 'A' and (resid 3566 through 3651 )
8X-RAY DIFFRACTION8chain 'A' and (resid 3652 through 3754 )

+
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