[English] 日本語
Yorodumi
- PDB-3bbz: Structure of the nucleocapsid-binding domain from the mumps virus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bbz
TitleStructure of the nucleocapsid-binding domain from the mumps virus phosphoprotein
ComponentsP protein
KeywordsVIRAL PROTEIN / REPLICATION / molten globule
Function / homologyP/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha / BROMIDE ION / FORMIC ACID / Phosphoprotein
Function and homology information
Biological speciesMumps virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsKingston, R.L. / Gay, L.S. / Baase, W.S. / Matthews, B.W.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of the nucleocapsid-binding domain from the mumps virus polymerase; an example of protein folding induced by crystallization
Authors: Kingston, R.L. / Gay, L.S. / Baase, W.S. / Matthews, B.W.
History
DepositionNov 11, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: P protein
B: P protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,34710
Polymers10,9112
Non-polymers4368
Water93752
1
A: P protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6735
Polymers5,4551
Non-polymers2184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: P protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6735
Polymers5,4551
Non-polymers2184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: P protein
hetero molecules

B: P protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,34710
Polymers10,9112
Non-polymers4368
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_845-x+3,y-1/2,-z+1/21
Buried area2500 Å2
ΔGint-9 kcal/mol
Surface area5750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.992, 55.485, 60.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide P protein / phosphoprotein


Mass: 5455.335 Da / Num. of mol.: 2 / Fragment: nucleocapsid-binding domain, UNP residues 343-391 / Mutation: C356S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mumps virus / Strain: Jeryl-Lynn vaccine / Plasmid: pET41A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star (DE3) / References: UniProt: Q9J4L6
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.7
Details: 0.2M Alanine/KOH pH 9.7, 3.6-4.6M Ammonium formate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.110.92
SYNCHROTRONSSRL BL9-120.954,0.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDDec 2, 2004
ADSC QUANTUM 3152CCDJun 27, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Double Crystal Si(111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
20.9541
30.9791
ReflectionResolution: 2.1→41.27 Å / Num. all: 4915 / Num. obs: 4915 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 5.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.4 / Num. unique all: 484 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→40.74 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.771 / SU ML: 0.154 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.318 / ESU R Free: 0.219 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 238 4.9 %RANDOM
Rwork0.18994 ---
all0.19254 4915 --
obs0.19254 4677 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.779 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms751 0 2 70 823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022766
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9781013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.487596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55925.62532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.51515165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.897156
X-RAY DIFFRACTIONr_chiral_restr0.1040.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02528
X-RAY DIFFRACTIONr_nbd_refined0.2180.2310
X-RAY DIFFRACTIONr_nbtor_refined0.290.2516
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.215
X-RAY DIFFRACTIONr_mcbond_it1.3621.5522
X-RAY DIFFRACTIONr_mcangle_it1.9542778
X-RAY DIFFRACTIONr_scbond_it2.9663279
X-RAY DIFFRACTIONr_scangle_it4.3944.5234
LS refinement shellHighest resolution: 2.1 Å / Num. reflection Rwork: 345 / Total num. of bins used: 20

+
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