[English] 日本語
Yorodumi
- PDB-4zdn: Streptomyces platensis isomigrastatin ketosynthase domain MgsF KS4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zdn
TitleStreptomyces platensis isomigrastatin ketosynthase domain MgsF KS4
ComponentsAT-less polyketide synthase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / NATPRO / MGSF / 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 / SAD / Resolution: 2.509 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
DepositionApr 17, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionMay 13, 2015ID: 4TL2
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Derived calculations / Structure summary
Revision 1.2Mar 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)67,9463
Polymers67,6721
Non-polymers2742
Water2,270126
1
A: AT-less polyketide synthase
hetero molecules

A: AT-less polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,8916
Polymers135,3442
Non-polymers5484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area4920 Å2
ΔGint-22 kcal/mol
Surface area42340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.685, 126.685, 143.681
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

-
Components

#1: Protein AT-less polyketide synthase


Mass: 67671.812 Da / Num. of mol.: 1 / Fragment: RESIDUES 550-1188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces platensis subsp. rosaceus (bacteria)
Plasmid: PMCSG68 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: D0U2E4
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 4.28 Å3/Da / Density % sol: 71.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1M SODIUM MALONATE, 0.1M HEPES PH7.0, 0.5% JEFFAMINE ED2001
PH range: 7

-
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: 2.509→50 Å / Num. obs: 40687 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 38.56 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 8.9
Reflection shellResolution: 2.509→2.55 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.973 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
HKL-3000data reduction
HKL-3000phasing
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.509→40.515 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.92 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 3306 5 %Random selection
Rwork0.1874 ---
obs0.1893 66176 86.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.509→40.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4355 0 16 126 4497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034494
X-RAY DIFFRACTIONf_angle_d0.6616137
X-RAY DIFFRACTIONf_dihedral_angle_d10.7181576
X-RAY DIFFRACTIONf_chiral_restr0.025665
X-RAY DIFFRACTIONf_plane_restr0.003820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5086-2.54440.2644580.26211136X-RAY DIFFRACTION38
2.5444-2.58240.358620.26061321X-RAY DIFFRACTION43
2.5824-2.62270.3221810.27241418X-RAY DIFFRACTION47
2.6227-2.66570.3539760.27621613X-RAY DIFFRACTION53
2.6657-2.71170.2931020.29041840X-RAY DIFFRACTION61
2.7117-2.7610.35421300.28932189X-RAY DIFFRACTION72
2.761-2.81410.31361230.2872548X-RAY DIFFRACTION84
2.8141-2.87150.37161490.28772731X-RAY DIFFRACTION90
2.8715-2.93390.30641800.28062897X-RAY DIFFRACTION97
2.9339-3.00210.30361520.26753004X-RAY DIFFRACTION99
3.0021-3.07720.32681680.26013023X-RAY DIFFRACTION99
3.0772-3.16040.35761590.24042969X-RAY DIFFRACTION99
3.1604-3.25330.29361400.22943044X-RAY DIFFRACTION99
3.2533-3.35830.2561470.22193029X-RAY DIFFRACTION100
3.3583-3.47830.22851650.19642998X-RAY DIFFRACTION99
3.4783-3.61740.20281520.18153006X-RAY DIFFRACTION99
3.6174-3.7820.23181470.16533017X-RAY DIFFRACTION99
3.782-3.98120.15421660.14343011X-RAY DIFFRACTION99
3.9812-4.23040.17811300.13343016X-RAY DIFFRACTION99
4.2304-4.55660.12771650.12223017X-RAY DIFFRACTION100
4.5566-5.01440.16761510.1283013X-RAY DIFFRACTION99
5.0144-5.73820.19971680.15623038X-RAY DIFFRACTION100
5.7382-7.22290.18691430.16523030X-RAY DIFFRACTION100
7.2229-40.520.1891920.15422962X-RAY DIFFRACTION99
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)
12.1261-0.35440.65352.3194-0.92112.18050.06710.3157-0.3963-0.2756-0.11930.4160.28-1.0513-0.0510.19340.0397-0.00580.8591-0.16520.41831.773110.71587.2303
21.9462-1.4402-0.16423.0409-1.15561.8085-0.21330.0971-0.32060.53970.25930.280.0596-0.2238-0.04680.45930.18780.02560.4577-0.06380.325734.667318.422321.5879
30.9939-1.1527-0.52652.2447-0.64882.0518-0.12640.5444-0.0687-0.14020.06880.3391-0.2107-0.76440.06760.34020.2613-0.03770.8617-0.0470.305231.272622.81786.3264
45.5836-1.88080.56072.4974-0.37390.26560.10340.4020.578-0.1472-0.1204-0.0961-0.5138-0.22070.00690.50870.41870.06210.7010.08010.316334.465135.59013.4902
52.1062-0.8120.30622.4987-0.19672.1203-0.05690.92920.123-0.7004-0.0935-0.1571-0.5074-0.3695-0.09390.40530.43690.01710.98310.03220.25838.834527.9104-6.3526
62.1012-1.09410.36882.48421.37062.54460.12510.20990.022-0.2164-0.2125-0.102-0.24810.22360.05730.1274-0.0390.02720.34650.05140.216759.49735.793113.1953
72.0123-0.2274-0.38810.1891-0.74333.7806-0.0155-0.01130.0211-0.0121-0.174-0.0886-0.10260.65970.11540.1409-0.00430.01880.26570.04890.310964.57011.127124.6208
84.2198-1.54060.65592.0129-0.4213.0761-0.01810.0955-0.0560.1163-0.1911-0.1017-0.21240.10490.0690.1347-0.06970.04640.3510.05730.209257.04986.674720.2203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 551 through 658 )
2X-RAY DIFFRACTION2chain 'A' and (resid 659 through 725 )
3X-RAY DIFFRACTION3chain 'A' and (resid 726 through 807 )
4X-RAY DIFFRACTION4chain 'A' and (resid 808 through 849 )
5X-RAY DIFFRACTION5chain 'A' and (resid 850 through 991 )
6X-RAY DIFFRACTION6chain 'A' and (resid 992 through 1055 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1056 through 1132 )
8X-RAY DIFFRACTION8chain 'A' and (resid 1133 through 1180 )

+
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