[English] 日本語
Yorodumi
- PDB-7kd4: Structure of the C-terminal domain of the Menangle virus phosphop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kd4
TitleStructure of the C-terminal domain of the Menangle virus phosphoprotein (residues 329 -388), fused to MBP. Space group P21.
ComponentsMaltodextrin-binding protein and Phosphoprotein fusion protein
KeywordsVIRAL PROTEIN / Paramyxovirus / Pararubulavirus / RNA-dependent RNA polymerase
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / periplasmic space
Similarity search - Function
Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ACP-like superfamily ...Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
alpha-maltose / Maltodextrin-binding protein / Phosphoprotein
Similarity search - Component
Biological speciesSerratia sp. (bacteria)
Menangle virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.312 Å
AuthorsWebby, M.N. / Kingston, R.L.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden FundUOA1202 New Zealand
CitationJournal: Viruses / Year: 2021
Title: Structural Analysis of the Menangle Virus P Protein Reveals a Soft Boundary between Ordered and Disordered Regions.
Authors: Webby, M.N. / Herr, N. / Bulloch, E.M.M. / Schmitz, M. / Keown, J.R. / Goldstone, D.C. / Kingston, R.L.
History
DepositionOct 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltodextrin-binding protein and Phosphoprotein fusion protein
B: Maltodextrin-binding protein and Phosphoprotein fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,48720
Polymers94,2652
Non-polymers2,22218
Water23,7981321
1
A: Maltodextrin-binding protein and Phosphoprotein fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,33911
Polymers47,1331
Non-polymers1,20710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltodextrin-binding protein and Phosphoprotein fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1479
Polymers47,1331
Non-polymers1,0158
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.561, 70.074, 111.739
Angle α, β, γ (deg.)90.000, 96.472, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Maltodextrin-binding protein and Phosphoprotein fusion protein


Mass: 47132.539 Da / Num. of mol.: 2 / Mutation: C352S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia sp. (strain FS14) (bacteria), (gene. exp.) Menangle virus
Strain: FS14 / Gene: malE, JW3994, V/P / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P1LXE0, UniProt: Q91MK1
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1321 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.65 M Ammonium sulphate, 0.2M Malic acid/KOH pH 5.5, Crystals were transferred into the following cryo-protective solution before vitrification: 1.65 M Ammonium sulphate, 0.2M Malic ...Details: 1.65 M Ammonium sulphate, 0.2M Malic acid/KOH pH 5.5, Crystals were transferred into the following cryo-protective solution before vitrification: 1.65 M Ammonium sulphate, 0.2M Malic acid/KOH pH 5.5, 5mM Maltose, 1 M Lithium sulfate

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.31→59.33 Å / Num. obs: 149703 / % possible obs: 70.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 12.824 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Net I/σ(I): 10.9
Reflection shellResolution: 1.31→1.33 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.607 / Num. unique obs: 307 / CC1/2: 0.783 / CC star: 0.937 / Rpim(I) all: 0.605 / Rrim(I) all: 0.857 / % possible all: 2.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230 2018/03/05refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4kyc

4kyc


Resolution: 1.312→59.329 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.221 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.08 / ESU R Free: 0.071
RfactorNum. reflection% reflectionSelection details
Rfree0.1957 7389 -Random Selection
Rwork0.1498 142138 --
all0.152 ---
obs-149527 71.002 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.824 Å2
Baniso -1Baniso -2Baniso -3
1--0.787 Å20 Å2-0.763 Å2
2---0.354 Å20 Å2
3---1.281 Å2
Refinement stepCycle: LAST / Resolution: 1.312→59.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6636 0 126 1321 8083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0127324
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.66110023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.475988
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48724.471340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58151310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6251525
X-RAY DIFFRACTIONr_chiral_restr0.0980.2997
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025498
X-RAY DIFFRACTIONr_nbd_refined0.1990.23699
X-RAY DIFFRACTIONr_nbtor_refined0.3110.24933
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2918
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2370.2129
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1820.2113
X-RAY DIFFRACTIONr_mcbond_it1.1391.0163585
X-RAY DIFFRACTIONr_mcangle_it1.4881.5324512
X-RAY DIFFRACTIONr_scbond_it1.8631.2483739
X-RAY DIFFRACTIONr_scangle_it2.2771.7985449
X-RAY DIFFRACTIONr_lrange_it3.19616.39312090
X-RAY DIFFRACTIONr_sphericity_free24.2465795
X-RAY DIFFRACTIONr_sphericity_bonded10.99557668
X-RAY DIFFRACTIONr_rigid_bond_restr1.73737324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.312-1.3460.426440.407779X-RAY DIFFRACTION5.2899
1.346-1.3830.3541130.2762315X-RAY DIFFRACTION16.1651
1.383-1.4230.2352170.2133913X-RAY DIFFRACTION28.0057
1.423-1.4670.2452890.1855515X-RAY DIFFRACTION40.6101
1.467-1.5150.2113650.1567142X-RAY DIFFRACTION53.8599
1.515-1.5680.1934550.1328533X-RAY DIFFRACTION67.442
1.568-1.6270.1865340.1229913X-RAY DIFFRACTION80.8341
1.627-1.6940.1776060.11211399X-RAY DIFFRACTION96.1015
1.694-1.7690.1695800.111293X-RAY DIFFRACTION99.8738
1.769-1.8550.1795700.11110870X-RAY DIFFRACTION99.965
1.855-1.9560.2355560.16610257X-RAY DIFFRACTION99.4299
1.956-2.0740.1684820.1369823X-RAY DIFFRACTION99.9709
2.074-2.2180.1764860.1429173X-RAY DIFFRACTION99.711
2.218-2.3950.2384220.1828545X-RAY DIFFRACTION99.2144
2.395-2.6240.1863960.1367867X-RAY DIFFRACTION99.8429
2.624-2.9330.1973600.1557172X-RAY DIFFRACTION99.9204
2.933-3.3860.193170.1556344X-RAY DIFFRACTION99.6708
3.386-4.1460.1662530.1375141X-RAY DIFFRACTION96.047
4.146-5.8580.2012330.1694061X-RAY DIFFRACTION97.7019
5.858-59.3290.2951110.2962083X-RAY DIFFRACTION88.8619

+
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