[English] 日本語
Yorodumi
- PDB-5czd: The complex structure of VinK with VinL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5czd
TitleThe complex structure of VinK with VinL
Components
  • Acyl-carrier-protein
  • Malonyl-CoA-[acyl-carrier-protein] transacylase
KeywordsTRANSFERASE / acyl carrier protein / polyketide biosynthesis
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid biosynthetic process / metal ion binding
Similarity search - Function
: / VinK acyltransferase small domain / : / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / ACP-like / Acyl transferase domain superfamily / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl transferase/acyl hydrolase/lysophospholipase / Phosphopantetheine attachment site ...: / VinK acyltransferase small domain / : / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / ACP-like / Acyl transferase domain superfamily / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl transferase/acyl hydrolase/lysophospholipase / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,1'-ethane-1,2-diyldipyrrolidine-2,5-dione / 4'-PHOSPHOPANTETHEINE / Acyl-carrier-protein / [acyl-carrier-protein] S-malonyltransferase
Similarity search - Component
Biological speciesStreptomyces halstedii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsMiyanaga, A. / Iwasawa, S. / Shinohara, Y. / Kudo, F. / Eguchi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K18679 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure-based analysis of the molecular interactions between acyltransferase and acyl carrier protein in vicenistatin biosynthesis.
Authors: Miyanaga, A. / Iwasawa, S. / Shinohara, Y. / Kudo, F. / Eguchi, T.
History
DepositionJul 31, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Malonyl-CoA-[acyl-carrier-protein] transacylase
B: Acyl-carrier-protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6524
Polymers48,0692
Non-polymers5832
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-22 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.140, 68.230, 148.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Malonyl-CoA-[acyl-carrier-protein] transacylase


Mass: 38170.207 Da / Num. of mol.: 1 / Mutation: S266C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinK / Plasmid: pCold I / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76KY5
#2: Protein Acyl-carrier-protein


Mass: 9898.995 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinL / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76KY4
#3: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#4: Chemical ChemComp-1N2 / 1,1'-ethane-1,2-diyldipyrrolidine-2,5-dione


Mass: 224.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.05 M magnesium chloride, 20% polyethylene glycol 8000, 0.1 M Tris-HCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 22, 2014
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.337→68.23 Å / Num. obs: 19598 / % possible obs: 99.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.1
Reflection shellResolution: 2.337→2.46 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 2.1 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CZC

5czc


Resolution: 2.34→62.07 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.9 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27287 1007 5.2 %RANDOM
Rwork0.20161 ---
obs0.20528 18539 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.586 Å2
Baniso -1Baniso -2Baniso -3
1--4.37 Å2-0 Å20 Å2
2--3.26 Å2-0 Å2
3---1.11 Å2
Refinement stepCycle: 1 / Resolution: 2.34→62.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2977 0 37 77 3091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193080
X-RAY DIFFRACTIONr_bond_other_d0.0060.022883
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9724184
X-RAY DIFFRACTIONr_angle_other_deg0.8383.0016608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2245376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.91923.108148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5415492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2681529
X-RAY DIFFRACTIONr_chiral_restr0.080.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213487
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02722
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.337→2.398 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 79 -
Rwork0.33 1301 -
obs--97.25 %

+
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