[English] 日本語
Yorodumi
- PDB-1yjg: Variable Small Protein 1 of Borrelia turicatae (VspA or Vsp1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yjg
TitleVariable Small Protein 1 of Borrelia turicatae (VspA or Vsp1)
ComponentsSurface protein VspA
KeywordsIMMUNE SYSTEM / helical bundle
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Lipoprotein, type 6 / Lipoprotein, OspC-type / Outer surface protein C-like superfamily / Lipoprotein / Four Helix Bundle (Hemerythrin (Met), subunit A) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Surface protein VspA
Similarity search - Component
Biological speciesBorrelia turicatae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsZueckert, W.R. / Yung, B.H. / Barbour, A.G. / Lawson, C.L.
Citation
Journal: J.Bacteriol. / Year: 2006
Title: Crystal structure of neurotropism-associated variable surface protein 1 (Vsp1) of Borrelia turicatae.
Authors: Lawson, C.L. / Yung, B.H. / Barbour, A.G. / Zuckert, W.R.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Structural Conservation of Neurotropism-associated VspA within the Variable Vsp-OspC Lipoprotein Family
Authors: Zueckert, W.R. / Kerentseva, T.A. / Lawson, C.L. / Barbour, A.G.
History
DepositionJan 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 400COMPOUND THIS PROTEIN WAS ORIGINALLY CALLED VARIABLE MEMBRANE PROTEIN A, OR VMPA. IN 2000, WHEN ...COMPOUND THIS PROTEIN WAS ORIGINALLY CALLED VARIABLE MEMBRANE PROTEIN A, OR VMPA. IN 2000, WHEN BORRELIA VMP GENES WERE RECLASSIFIED AS VSP OR VLP GENES, THE PROTEIN NAME WAS REVISED TO VARIABLE SMALL PROTEIN A (VSPA). IN 2002, TO ADDRESS PROBLEMS RELATED TO ALPHABETICAL NAMING OF MORE THAN ONE VSP GENE EXPRESSED AT THE SAME EXPRESSION SITE, THE PROTEIN NAME WAS FURTHER REVISED TO VARIABLE SMALL PROTEIN 1 (VSP1).

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Surface protein VspA
B: Surface protein VspA
D: Surface protein VspA
E: Surface protein VspA


Theoretical massNumber of molelcules
Total (without water)64,9664
Polymers64,9664
Non-polymers00
Water3,891216
1
A: Surface protein VspA
B: Surface protein VspA


Theoretical massNumber of molelcules
Total (without water)32,4832
Polymers32,4832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-26 kcal/mol
Surface area13380 Å2
MethodPISA
2
D: Surface protein VspA
E: Surface protein VspA


Theoretical massNumber of molelcules
Total (without water)32,4832
Polymers32,4832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-29 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.857, 34.213, 99.386
Angle α, β, γ (deg.)90.00, 112.68, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D
41E
51A
61B
71D
81E

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYS2AA57 - 11513 - 71
21SERSERLYSLYS2BB57 - 11513 - 71
31SERSERLYSLYS2DC57 - 11513 - 71
41SERSERLYSLYS2ED57 - 11513 - 71
52ASPASPTHRTHR3AA121 - 18877 - 144
62ASPASPTHRTHR3BB121 - 18877 - 144
72ASPASPTHRTHR3DC121 - 18877 - 144
82ASPASPTHRTHR3ED121 - 18877 - 144

-
Components

#1: Protein
Surface protein VspA


Mass: 16241.504 Da / Num. of mol.: 4 / Fragment: vspA core residues 45-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia turicatae (bacteria) / Gene: VspA / Plasmid: pET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O34000
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 25% (w/v) PEG 4000, 0.1 M LiCl, and 0.1 mM taurine, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2004 / Details: Si Monochromator
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 26408 / Num. obs: 26408 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.93 % / Rmerge(I) obs: 0.05 / Rsym value: 0.047 / Net I/σ(I): 26
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 2.68 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2308 / Rsym value: 0.161 / % possible all: 84.5

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Partially refined model for VspA 34-214, derived by molecular replacement starting from Borrelia burgdorferi OspC, strain B31 (PDB ID 1GGQ)

1ggq


Resolution: 2.22→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.903 / SU B: 7.7 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: isotropic B factors TLS groups. 4 TLS groups, Each chain = 1 TLS group
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.413 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26486 1329 5 %RANDOM
Rwork0.20577 ---
all0.20875 26240 --
obs0.20875 25078 95.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.726 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å2-1.82 Å2
2--2.03 Å20 Å2
3----2.22 Å2
Refinement stepCycle: LAST / Resolution: 2.22→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4508 0 0 216 4724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224520
X-RAY DIFFRACTIONr_bond_other_d0.0020.024326
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.9866087
X-RAY DIFFRACTIONr_angle_other_deg0.752310168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg0.7645622
X-RAY DIFFRACTIONr_chiral_restr0.0740.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024946
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02686
X-RAY DIFFRACTIONr_nbd_refined0.190.21150
X-RAY DIFFRACTIONr_nbd_other0.2070.24874
X-RAY DIFFRACTIONr_nbtor_other0.0860.22658
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2202
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.213
X-RAY DIFFRACTIONr_mcbond_it1.9233094
X-RAY DIFFRACTIONr_mcangle_it2.77954930
X-RAY DIFFRACTIONr_scbond_it2.06531426
X-RAY DIFFRACTIONr_scangle_it3.0551157
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A754tight positional0.140.2
2B754tight positional0.190.2
3D754tight positional0.180.2
4E754tight positional0.160.2
1A501medium positional0.270.5
2B501medium positional0.270.5
3D501medium positional0.290.5
4E501medium positional0.310.5
1A563loose positional0.410
2B563loose positional0.4110
3D563loose positional0.3710
4E563loose positional0.4510
1A754tight thermal3.135
2B754tight thermal2.125
3D754tight thermal2.285
4E754tight thermal2.985
1A501medium thermal3.7915
2B501medium thermal2.6215
3D501medium thermal3.0215
4E501medium thermal3.6115
1A563loose thermal4.9625
2B563loose thermal3.6625
3D563loose thermal2.9425
4E563loose thermal4.5425
LS refinement shellResolution: 2.222→2.28 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.289 66
Rwork0.247 1587
obs-1653
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)
10.54650.22010.2450.547-0.67281.38810.1119-0.0759-0.0312-0.0717-0.1314-0.0149-0.00290.08380.01950.2380.01890.02460.106-0.00970.15523.778-3.12222.4
21.83610.55441.3940.440.03260.5166-0.0908-0.19380.25190.0045-0.1738-0.1237-0.14180.2140.26460.2197-0.039-0.00190.1530.06020.188717.9073.3329.032
30.65360.2413-0.66661.6208-1.10161.27120.0215-0.02970.0362-0.0743-0.0799-0.16870.00510.06690.05840.2577-0.02190.05750.06450.03610.200424.612.405-18.245
41.5119-0.86880.10461.1995-0.15870.4431-0.00160.22560.2063-0.079-0.0986-0.41360.03810.19650.10020.2361-0.05440.12470.07460.09090.296539.955.142-20.261
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA45 - 2011 - 157
2X-RAY DIFFRACTION2BB45 - 2011 - 157
3X-RAY DIFFRACTION3DC47 - 2013 - 157
4X-RAY DIFFRACTION4ED45 - 2011 - 157

+
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