[English] 日本語
Yorodumi
- PDB-8f47: Crystal structure of VACV D13 in complex with STK69439 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8f47
TitleCrystal structure of VACV D13 in complex with STK69439
ComponentsScaffold protein D13Scaffolding
KeywordsVIRAL PROTEIN / poxvirus / assembly / scaffolding protein / Fragment-based drug design / immature virion
Function / homologyPoxvirus rifampicin-resistance / Poxvirus rifampicin resistance protein / response to antibiotic / membrane / identical protein binding / FORMIC ACID / 6,8-dimethoxy-2-methylquinolin-4-amine / Scaffold protein OPG125
Function and homology information
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSubedi, B.P. / Garriga, D. / Coulibaly, F.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1051907 Australia
Citation
Journal: To Be Published
Title: Structure of scaffolidng protein D13 of Vaccinia Virus in complex with fragments inhibiting A17 binding.
Authors: Subedi, B.P. / Garriga, D. / Coulibaly, F.
#1: Journal: Proc Natl Acad Sci U S A / Year: 2018
Title: Structural basis for the inhibition of poxvirus assembly by the antibiotic rifampicin.
Authors: Garriga, D. / Headey, S. / Accurso, C. / Gunzburg, M. / Scanlon, M. / Coulibaly, F.
History
DepositionNov 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Scaffold protein D13
B: Scaffold protein D13
C: Scaffold protein D13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,52129
Polymers195,1533
Non-polymers1,36926
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)190.522, 190.522, 257.948
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 or (resid 5 and (name...
d_2ens_1(chain "B" and (resid 4 or (resid 5 and (name...
d_3ens_1(chain "C" and (resid 4 through 9 or resid 16...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRGLYA5 - 73
d_12ens_1PHEILEA75 - 183
d_13ens_1ASPGLUA185 - 308
d_14ens_1GLYASNA310 - 506
d_15ens_1PROMETA508 - 538
d_16ens_1FMTFMTC
d_17ens_1FMTFMTD
d_18ens_1FMTFMTE
d_19ens_1FMTFMTF
d_21ens_1THRLEUG5 - 10
d_22ens_1ILEASNG13 - 42
d_23ens_1ASNGLYG45 - 77
d_24ens_1PHEILEG79 - 187
d_25ens_1ASPGLUG189 - 312
d_26ens_1GLYASNG314 - 510
d_27ens_1PROMETG512 - 542
d_28ens_1FMTFMTH
d_29ens_1FMTFMTI
d_210ens_1FMTFMTJ
d_211ens_1FMTFMTK
d_31ens_1THRLEUL1 - 6
d_32ens_1ILEGLYL8 - 70
d_33ens_1PHEILEL72 - 180
d_34ens_1ASPGLUL182 - 305
d_35ens_1GLYASNL307 - 503
d_36ens_1PROMETL505 - 535
d_37ens_1FMTFMTO
d_38ens_1FMTFMTP
d_39ens_1FMTFMTQ
d_310ens_1FMTFMTR

NCS oper:
IDCodeMatrixVector
1given(-0.245511858376, -0.747643372423, -0.617052116979), (0.832974114858, -0.488301767857, 0.260222034969), (-0.495860919384, -0.450100845566, 0.742651450849)219.449722054, 65.7890516665, 103.509110556
2given(-0.255921329971, 0.826910115661, -0.50072341016), (-0.7355516593, -0.502672138672, -0.454185510011), (-0.627270300083, 0.252072175418, 0.736879629935)52.5661482557, 242.747776064, 43.6128582487

-
Components

#1: Protein Scaffold protein D13 / Scaffolding / 62 kDa protein / Rifampicin resistance protein


Mass: 65050.840 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Gene: VACWR118, D13L
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P68440
#2: Chemical...
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-XDF / 6,8-dimethoxy-2-methylquinolin-4-amine


Mass: 218.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 3.46 Å3/Da / Density % sol: 64.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 1.7 - 2.2 M sodium formate and 0.1 M citric acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.1→47.63 Å / Num. obs: 50722 / % possible obs: 100 % / Redundancy: 22 % / Biso Wilson estimate: 56.8 Å2 / CC1/2: 0.993 / Net I/σ(I): 13.1
Reflection shellResolution: 3.1→3.2 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4589 / CC1/2: 0.733 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20rc4_4425refinement
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BEI

6bei


Resolution: 3.1→26.04 Å / SU ML: 0.3983 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 2537 5.02 %
Rwork0.1677 48008 -
obs0.1709 50545 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.37 Å2
Refinement stepCycle: LAST / Resolution: 3.1→26.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12687 0 91 276 13054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010413101
X-RAY DIFFRACTIONf_angle_d1.134217808
X-RAY DIFFRACTIONf_chiral_restr0.06792068
X-RAY DIFFRACTIONf_plane_restr0.00922279
X-RAY DIFFRACTIONf_dihedral_angle_d5.12921783
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.77277435148
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.639354499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.160.35041430.26642615X-RAY DIFFRACTION100
3.16-3.220.32851280.24822636X-RAY DIFFRACTION100
3.22-3.290.31251220.23452651X-RAY DIFFRACTION100
3.29-3.370.2991370.21082625X-RAY DIFFRACTION100
3.37-3.450.26781560.19452594X-RAY DIFFRACTION100
3.45-3.550.26241440.17742628X-RAY DIFFRACTION99.96
3.55-3.650.22261580.17332612X-RAY DIFFRACTION100
3.65-3.770.26231520.16362617X-RAY DIFFRACTION100
3.77-3.90.21751320.15572655X-RAY DIFFRACTION100
3.9-4.060.2181370.14452645X-RAY DIFFRACTION100
4.06-4.240.22031160.13612669X-RAY DIFFRACTION100
4.24-4.470.1681330.11982675X-RAY DIFFRACTION100
4.47-4.740.18231320.12032668X-RAY DIFFRACTION100
4.74-5.110.1681420.12232678X-RAY DIFFRACTION100
5.11-5.620.21381620.13972683X-RAY DIFFRACTION100
5.62-6.420.18161420.15962713X-RAY DIFFRACTION100
6.42-8.050.241430.18762757X-RAY DIFFRACTION100
8.05-26.040.27271580.21822887X-RAY DIFFRACTION99.64

+
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