[English] 日本語
Yorodumi
- PDB-1t6v: Crystal structure analysis of the nurse shark new antigen recepto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t6v
TitleCrystal structure analysis of the nurse shark new antigen receptor (NAR) variable domain in complex with lysozyme
Components
  • Lysozyme C
  • novel antigen receptor
KeywordsHYDROLASE/IMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / PROTEIN-PROTEIN COMPLEX / HYDROLASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Immunoglobulin V-Type / Immunoglobulin V-set domain ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Immunoglobulin V-Type / Immunoglobulin V-set domain / Lysozyme / Immunoglobulin V-set domain / Lysozyme-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Lysozyme C / Novel antigen receptor
Similarity search - Component
Biological speciesGinglymostoma cirratum (nurse shark)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsStanfield, R.L. / Dooley, H. / Flajnik, M.F. / Wilson, I.A.
CitationJournal: Science / Year: 2004
Title: Crystal structure of a shark single-domain antibody V region in complex with lysozyme.
Authors: Stanfield, R.L. / Dooley, H. / Flajnik, M.F. / Wilson, I.A.
History
DepositionMay 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Lysozyme C
N: novel antigen receptor
M: Lysozyme C
O: novel antigen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8446
Polymers52,7734
Non-polymers712
Water5,206289
1
L: Lysozyme C
N: novel antigen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4223
Polymers26,3862
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-11 kcal/mol
Surface area11070 Å2
MethodPISA
2
M: Lysozyme C
O: novel antigen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4223
Polymers26,3862
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.79, 113.81, 58.44
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d 4 / Gal d IV


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: hen egg white / References: UniProt: P00698, lysozyme
#2: Protein novel antigen receptor


Mass: 12055.245 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginglymostoma cirratum (nurse shark) / Plasmid: PIMS100 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: Q8AXI4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15% PEG 10,000, 0.1M imidazole malate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.7→46.1 Å / Num. all: 54344 / Num. obs: 54344 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 12 Å2 / Rsym value: 0.09 / Net I/σ(I): 14.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2730 / Rsym value: 0.497 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SQ2

1sq2


Resolution: 1.7→46.1 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.834 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22076 2559 4.7 %RANDOM
Rwork0.19402 ---
all0.19527 51760 --
obs0.19527 51760 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.691 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3670 0 2 289 3961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0213744
X-RAY DIFFRACTIONr_bond_other_d0.0010.023248
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.9245062
X-RAY DIFFRACTIONr_angle_other_deg0.97937528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04223.103174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13115612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2431538
X-RAY DIFFRACTIONr_chiral_restr0.1270.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024270
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02818
X-RAY DIFFRACTIONr_nbd_refined0.2240.2676
X-RAY DIFFRACTIONr_nbd_other0.1990.23244
X-RAY DIFFRACTIONr_nbtor_other0.0850.22315
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2191
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.28
X-RAY DIFFRACTIONr_mcbond_it1.511.52995
X-RAY DIFFRACTIONr_mcbond_other0.3741.51020
X-RAY DIFFRACTIONr_mcangle_it1.81523744
X-RAY DIFFRACTIONr_scbond_it3.02431663
X-RAY DIFFRACTIONr_scangle_it4.0634.51318
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 193
Rwork0.223 3704

+
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