[English] 日本語
Yorodumi
- PDB-7f2r: Crystal structure of VinK-VinL covalent complex formed with a pan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7f2r
TitleCrystal structure of VinK-VinL covalent complex formed with a pantetheineamide cross-linking probe
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 / cytosol
Similarity search - Function
: / VinK acyltransferase small domain / Acyl transferase domain superfamily / 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
Similarity search - Domain/homology
Chem-9EF / Acyl-carrier-protein / [acyl-carrier-protein] S-malonyltransferase
Similarity search - Component
Biological speciesStreptomyces halstedii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMiyanaga, A. / Ouchi, R. / Kudo, F. / Eguchi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H02911 Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Complex structure of the acyltransferase VinK and the carrier protein VinL with a pantetheine cross-linking probe.
Authors: Miyanaga, A. / Ouchi, R. / Kudo, F. / Eguchi, T.
History
DepositionJun 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,1116
Polymers92,3444
Non-polymers7672
Water12,412689
1
A: Malonyl-CoA-[acyl-carrier-protein] transacylase
B: Acyl-carrier-protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5553
Polymers46,1722
Non-polymers3831
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-10 kcal/mol
Surface area16830 Å2
MethodPISA
2
C: Malonyl-CoA-[acyl-carrier-protein] transacylase
D: Acyl-carrier-protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5553
Polymers46,1722
Non-polymers3831
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-10 kcal/mol
Surface area16810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.282, 148.224, 68.791
Angle α, β, γ (deg.)90.000, 91.080, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAPROPROAA18 - 32019 - 321
221ALAALAPROPROCC18 - 32019 - 321
132METMETGLUGLUBB1 - 794 - 82
242METMETGLUGLUDD1 - 794 - 82

NCS ensembles :
ID
1
2

-
Components

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


Mass: 36273.078 Da / Num. of mol.: 2 / Mutation: S106C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinK / Plasmid: pCold I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76KY5
#2: Protein Acyl-carrier-protein


Mass: 9898.995 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinL / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76KY4
#3: Chemical ChemComp-9EF / N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 383.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26N3O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG8000, magnesium chloride, Tris-HCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 29, 2021
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: 1.95→50 Å / Num. obs: 63757 / % possible obs: 99 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.065 / Net I/σ(I): 9.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2 / Num. unique obs: 4526 / CC1/2: 0.896 / Rrim(I) all: 0.462 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CZD

5czd


Resolution: 1.95→40.16 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.277 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 3149 4.9 %RANDOM
Rwork0.1933 ---
obs0.1957 60569 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.5 Å2 / Biso mean: 33.219 Å2 / Biso min: 19.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å21.66 Å2
2---0.38 Å20 Å2
3---1 Å2
Refinement stepCycle: final / Resolution: 1.95→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6004 0 48 689 6741
Biso mean--48.1 37.6 -
Num. residues----764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136186
X-RAY DIFFRACTIONr_bond_other_d0.0050.0175692
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.6518396
X-RAY DIFFRACTIONr_angle_other_deg1.6171.58613114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7565760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.91121.011356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27815990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1241558
X-RAY DIFFRACTIONr_chiral_restr0.1560.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026994
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021400
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A99460.06
12C99460.06
21B26140.07
22D26140.07
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 232 -
Rwork0.254 4505 -
all-4737 -
obs--99.87 %
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)
10.07430.0663-0.01690.3185-0.03980.27530.01740.01690.03620.03820.0130.00950.02210.0011-0.03050.02350.01740.04880.04390.0290.17483.5294.49735.004
21.41770.0688-1.09120.82510.58341.335-0.0613-0.0462-0.04090.04780.0543-0.02240.0740.07650.00690.07630.0270.02180.0146-0.01050.117510.623-22.30629.165
30.0642-0.0513-0.02120.2219-0.03340.3903-0.03720.0023-0.0254-0.01360.0098-0.0296-0.0092-0.00440.02740.0428-0.00030.06020.03470.0290.175825.65627.084-1.163
41.78740.3741.17890.53890.71461.2572-0.09110.03690.0237-0.00760.0829-0.0098-0.0590.09930.00820.1161-0.00480.03530.0138-0.00470.098932.43753.9865.19
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 320
2X-RAY DIFFRACTION2B1 - 101
3X-RAY DIFFRACTION3C18 - 320
4X-RAY DIFFRACTION4D1 - 101

+
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://pdbjlvh1.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