[English] 日本語
Yorodumi
- PDB-3t6s: Crystal structure of CerJ from Streptomyces tendae in Complex with CoA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t6s
TitleCrystal structure of CerJ from Streptomyces tendae in Complex with CoA
Components(CerJ) x 2
KeywordsTRANSFERASE / Thiloase superfamily / FabH-like fold / Acyltransferase / O-malonyl transferase
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces tendae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsZocher, G. / Bretschneider, T. / Hertweck, C. / Stehle, T.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: A ketosynthase homolog uses malonyl units to form esters in cervimycin biosynthesis.
Authors: Bretschneider, T. / Zocher, G. / Unger, M. / Scherlach, K. / Stehle, T. / Hertweck, C.
History
DepositionJul 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Feb 1, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CerJ
B: CerJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9443
Polymers75,1762
Non-polymers7681
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-43 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.910, 106.910, 122.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-385-

HOH

-
Components

#1: Protein CerJ


Mass: 37604.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces tendae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: H2L2M1*PLUS
#2: Protein CerJ


Mass: 37572.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces tendae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: H2L2M1*PLUS
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22.5% PEG 4000, 100 mM Tris/HCl pH 8.5, 200 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 27, 2010
RadiationMonochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 48366 / Num. obs: 48321 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3.73 / Num. unique all: 3522 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC- Rigid Bodyrefinement
XDSdata reduction
XSCALEdata scaling
REFMAC- Rigid Bodyphasing
RefinementResolution: 2→29.65 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 8.213 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19675 2413 5 %RANDOM
Rwork0.16018 ---
obs0.16198 45863 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.835 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--0.9 Å20 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 2→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5036 0 48 410 5494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215232
X-RAY DIFFRACTIONr_bond_other_d0.0010.023420
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9697156
X-RAY DIFFRACTIONr_angle_other_deg0.90238286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7575690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.02522.569218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48915739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2691549
X-RAY DIFFRACTIONr_chiral_restr0.0790.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216008
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021090
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_it1.21333390
X-RAY DIFFRACTIONr_mcbond_other0.45531410
X-RAY DIFFRACTIONr_mcangle_it1.7863.55378
X-RAY DIFFRACTIONr_scbond_it1.93141842
X-RAY DIFFRACTIONr_scangle_it2.7644.51774
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 174 -
Rwork0.215 3315 -
obs--100 %
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)
11.27280.55040.29251.3022-0.26041.27990.0946-0.13-0.07030.0322-0.0765-0.03780.03610.089-0.01810.03440.01920.02730.0490.03220.027520.5556.6727-26.5429
21.20920.2030.08631.5009-0.14781.21680.078-0.25350.3650.1879-0.09750.0179-0.32070.1330.01960.1582-0.03750.07520.1296-0.02440.166128.842734.2532-25.9491
30.66330.6312-0.01651.2458-0.1180.47050.01860.00250.0952-0.1007-0.00010.0732-0.03960.0372-0.01850.12380.0310.0510.15290.02160.122720.773717.3127-33.2195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 342
2X-RAY DIFFRACTION2B1 - 342
3X-RAY DIFFRACTION2B358
4X-RAY DIFFRACTION3A358 - 596
5X-RAY DIFFRACTION3B359 - 529

+
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