[English] 日本語
Yorodumi
- PDB-3twi: Variable Lymphocyte Receptor Recognition of the Immunodominant Gl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3twi
TitleVariable Lymphocyte Receptor Recognition of the Immunodominant Glycoprotein of Bacillus anthracis Spores
Components
  • BclA protein
  • Variable lymphocyte receptor B
KeywordsIMMUNE SYSTEM / Leucine-Rich Repeat / Antigen-binding / Secreted
Function / homology
Function and homology information


extracellular matrix structural constituent conferring tensile strength / regulation of phagocytosis / extracellular matrix organization / extracellular matrix / extracellular space / plasma membrane
Similarity search - Function
BclA, C-terminal domain / BclA C-terminal domain / Leader peptide, exosporium / : / : / Jelly Rolls - #40 / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Tumour necrosis factor-like domain superfamily ...BclA, C-terminal domain / BclA C-terminal domain / Leader peptide, exosporium / : / : / Jelly Rolls - #40 / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Variable lymphocyte receptor B / BclA protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
Petromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsKirchdoerfer, R.N. / Herrin, B.R. / Han, B.W. / Turnbough Jr., C.L. / Cooper, M.D. / Wilson, I.A.
CitationJournal: Structure / Year: 2012
Title: Variable Lymphocyte Receptor Recognition of the Immunodominant Glycoprotein of Bacillus anthracis Spores.
Authors: Kirchdoerfer, R.N. / Herrin, B.R. / Han, B.W. / Turnbough, C.L. / Cooper, M.D. / Wilson, I.A.
History
DepositionSep 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BclA protein
B: BclA protein
C: BclA protein
D: Variable lymphocyte receptor B
E: Variable lymphocyte receptor B
F: Variable lymphocyte receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9589
Polymers107,6816
Non-polymers2763
Water6,900383
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.809, 146.528, 209.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 6 / Auth seq-ID: 85 - 210 / Label seq-ID: 26 - 151

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

-
Components

#1: Protein BclA protein / Spore surface glycoprotein BclA


Mass: 16422.553 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN / Mutation: T185N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: bclA, BA_1222, GBAA_1222 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81JD7
#2: Protein Variable lymphocyte receptor B


Mass: 19471.273 Da / Num. of mol.: 3 / Fragment: ANTIGEN-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Gene: VLR-B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A9Z0I5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.26
Details: 15% PEG 6000, 1.2 M LiCl, 0.1 M sodium citrate, pH 5.26, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2010
RadiationMonochromator: Si(111), Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 37042 / Num. obs: 37042 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rsym value: 0.122 / Net I/σ(I): 9.5
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.581 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERfor MRphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2R6Q, 2R9U

2r6q

2r9u


Resolution: 2.55→41.88 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 19.502 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23293 1869 5.1 %RANDOM
Rwork0.18932 ---
obs0.19149 35031 96.69 %-
all-35031 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.948 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---1.47 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.55→41.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6289 0 18 383 6690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226411
X-RAY DIFFRACTIONr_bond_other_d00.023994
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.9738761
X-RAY DIFFRACTIONr_angle_other_deg4.41939962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4065835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.13526.268209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42915990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.503156
X-RAY DIFFRACTIONr_chiral_restr0.0620.21120
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216954
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021078
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it01.54241
X-RAY DIFFRACTIONr_mcbond_other01.51739
X-RAY DIFFRACTIONr_mcangle_it026888
X-RAY DIFFRACTIONr_scbond_it032170
X-RAY DIFFRACTIONr_scangle_it04.51873
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1424 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.335
2Bloose positional0.435
3Cloose positional0.365
1Aloose thermal010
2Bloose thermal010
3Cloose thermal010
LS refinement shellResolution: 2.55→2.613 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 131 -
Rwork0.291 2559 -
obs--95.32 %
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)
12.73640.5368-0.11182.3060.77942.32820.01970.17780.0055-0.15730.00470.0574-0.0411-0.1546-0.02440.07920.01350.0080.02660.02040.0735-3.0203-23.4728-45.7234
21.3139-0.09170.64822.44760.70491.9960.0267-0.0974-0.16570.1773-0.00720.18450.0613-0.183-0.01960.0861-0.01420.03970.09020.04650.0703-17.7877-32.4931-32.5302
31.85530.34860.12562.21360.72332.97040.0783-0.0577-0.2770.1308-0.086-0.24340.21210.09260.00770.05010.014-0.03780.0260.040.16121.7125-42.1915-35.5686
43.3963-1.6359-1.41694.71752.08722.95120.12890.28970.1707-0.3504-0.0357-0.3365-0.3314-0.0005-0.09320.0625-0.00460.00040.03670.03060.112717.1176-4.3912-48.5188
53.2638-0.3567-0.96182.5014-0.77768.72770.1591-0.14480.02240.05530.07940.3515-0.212-0.689-0.23840.17630.050.09820.22660.05040.1442-34.7048-17.6952-17.6256
610.6072.2740.01889.2415-1.07894.54880.1058-0.8688-1.37620.9862-0.1744-1.36560.65090.42830.06860.64520.1043-0.24040.57570.29060.762812.73-53.8107-15.4961
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A80 - 215
2X-RAY DIFFRACTION2B80 - 215
3X-RAY DIFFRACTION3C80 - 215
4X-RAY DIFFRACTION4D21 - 188
5X-RAY DIFFRACTION5E21 - 187
6X-RAY DIFFRACTION6F24 - 187

+
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