[English] 日本語
Yorodumi
- PDB-2w59: STRUCTURE OF AN AVIAN IGY-FC 3-4 FRAGMENT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2w59
TitleSTRUCTURE OF AN AVIAN IGY-FC 3-4 FRAGMENT
ComponentsIGY FCU3-4
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / AVIAN / IGY FC
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsFabiane, S.M. / Taylor, A.I. / Sutton, B.J. / Calvert, R.A.
CitationJournal: Biochemistry / Year: 2009
Title: The Crystal Structure of an Avian Igy-Fc Fragment Reveals Conservation with Both Mammalian Igg and Ige.
Authors: Taylor, A.I. / Fabiane, S.M. / Sutton, B.J. / Calvert, R.A.
History
DepositionDec 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Advisory / Category: database_PDB_caveat
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IGY FCU3-4
B: IGY FCU3-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,71110
Polymers50,9862
Non-polymers1,7268
Water10,016556
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint0 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.481, 80.140, 99.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody IGY FCU3-4


Mass: 25492.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PRY / Cell line (production host): NS0 / Production host: MUS MUSCULUS (house mouse)
#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATION C340S

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.88 % / Description: NONE
Crystal growDetails: FCU3-4 AT 3MG/ML, 40MM POTASSIUM PHOSPHATE, 16% PEG8000, 20% GLYCEROL. 100NL DROPS DISPENSED BY A MOSQUITO ROBOT ON MRC/WILDEN PLATES. PLATES KEPT AT 255K.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9698
DetectorType: ADSC CCD / Detector: CCD / Date: May 25, 2008 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9698 Å / Relative weight: 1
ReflectionResolution: 1.75→69.5 Å / Num. obs: 56233 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.9
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.8 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O0V

1o0v


Resolution: 1.75→49.57 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 17.25 / Stereochemistry target values: ML
Details: 22 TLS GROUPS. REFINEMENT SOFTWARE ADDS THE TLS COMPONENT TO THE ANISOU RECORD OF THE PDB FILE. ATOMIC TEMPERATURE FACTORS WERE NOT REFINED ANISOTROPICALLY.
RfactorNum. reflection% reflection
Rfree0.196 2818 5 %
Rwork0.169 --
obs0.171 56158 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.4 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.2408 Å20 Å20 Å2
2---4.3371 Å20 Å2
3---0.0963 Å2
Refinement stepCycle: LAST / Resolution: 1.75→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 114 556 4042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063628
X-RAY DIFFRACTIONf_angle_d1.0774953
X-RAY DIFFRACTIONf_dihedral_angle_d19.4211369
X-RAY DIFFRACTIONf_chiral_restr0.073572
X-RAY DIFFRACTIONf_plane_restr0.004623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.78020.2481350.22362643X-RAY DIFFRACTION99
1.7802-1.81260.24271320.21272624X-RAY DIFFRACTION99
1.8126-1.84740.22711440.20832611X-RAY DIFFRACTION100
1.8474-1.88510.23481390.19652655X-RAY DIFFRACTION100
1.8851-1.92610.20921470.17872648X-RAY DIFFRACTION100
1.9261-1.97090.17051210.16472647X-RAY DIFFRACTION100
1.9709-2.02020.17961360.15742656X-RAY DIFFRACTION100
2.0202-2.07480.1881460.15322642X-RAY DIFFRACTION100
2.0748-2.13590.1851530.1532651X-RAY DIFFRACTION100
2.1359-2.20480.18251490.15832646X-RAY DIFFRACTION100
2.2048-2.28360.18271370.15642672X-RAY DIFFRACTION100
2.2836-2.37510.19291510.16382622X-RAY DIFFRACTION100
2.3751-2.48320.2271570.17062689X-RAY DIFFRACTION100
2.4832-2.61410.2061560.16842649X-RAY DIFFRACTION100
2.6141-2.77780.20451280.16812717X-RAY DIFFRACTION100
2.7778-2.99230.20661310.16132697X-RAY DIFFRACTION100
2.9923-3.29340.17551350.15652712X-RAY DIFFRACTION100
3.2934-3.76980.17381300.14842725X-RAY DIFFRACTION100
3.7698-4.74890.14821370.14032720X-RAY DIFFRACTION99
4.7489-49.58720.21831540.20142714X-RAY DIFFRACTION94
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)
11.0382-0.25310.37851.189-0.37310.7053-0.0039-0.1193-0.20470.4559-0.2309-0.4557-0.08590.0496-0.02890.17880.01060.00810.22020.11750.2673-3.4654-1.89834.937
21.43510.0981-0.60550.8619-0.29560.40310.1828-0.0585-0.13990.2501-0.1415-0.48230.29960.8108-0.00030.36830.063-0.04480.43780.15010.4268.9129-4.108111.2523
3-0.0148-0.0249-0.03960.11180.08190.0417-0.16760.80330.008-0.22960.037-0.541-0.23760.35560.0020.7306-0.11030.43460.85230.21270.8629.683-2.9934-5.7904
43.8397-0.6625-0.38082.0774-0.5014-0.0530.15220.17080.4640.4776-0.2953-0.42860.06980.7237-0.00140.3313-0.02080.06490.18750.06920.36633.24770.04828.5958
51.0982-0.2091-1.33941.08410.06291.02830.3748-0.2616-0.76780.4434-0.187-0.47330.96710.36890.00750.43560.0837-0.03340.35070.06150.4687.4878-10.55748.8267
60.53750.36010.2321.91820.27381.646-0.0888-0.022-0.1099-0.09270.0285-0.07910.1770.000500.0490.01650.02590.05680.00020.0338-27.2168-3.17926.9014
71.4642-0.4051-0.15030.7294-0.18082.49560.03860.04220.0024-0.1377-0.0781-0.214-0.05280.0437-0.0096-0.00020.0180.03030.0572-0.00560.0146-21.30820.38187.4494
85.1349-1.1878-0.04581.8794-4.33274.2435-0.12611.072-1.7631-0.73340.06520.44131.9762-0.14370.31630.50460.01390.07880.1914-0.15430.4089-20.7916-18.16351.8151
90.77690.27350.26550.6098-0.15691.0297-0.03940.07190.1387-0.0761-0.0685-0.097-0.1337-0.1903-0.23880.00940.02460.04660.04120.0246-0.0083-27.60435.87368.1885
100.56090.75890.61091.15520.19441.8469-0.07610.5245-0.4242-0.3524-0.1530.2136-0.0064-0.3865-0.00680.12520.040.01340.1751-0.0150.0656-26.08372.3834-2.3793
110.1358-1.04860.43471.5474-0.32191.6555-0.10.26060.1485-0.2306-0.0656-0.4872-0.01680.371900.1006-0.0490.00940.17880.04580.1669-18.4362-18.406432.8963
120.64370.26861.04732.4028-0.57931.9936-0.23370.0928-0.05390.3182-0.0229-0.82050.51390.32570.00030.16670.0254-0.02850.26290.03760.2933-7.9651-22.552939.9667
130.3998-0.24110.53720.35850.04170.28760.46850.7375-0.22170.0061-0.4005-0.31430.4861-0.3833-0.00050.34220.06970.0170.1919-0.02110.2644-10.9852-29.923435.7628
141.94241.06742.27063.306-1.02392.1186-0.17870.2792-0.1885-0.3022-0.0392-0.6630.28460.4938-0.04440.1247-0.01830.05510.16190.03340.1377-12.9981-21.723634.5366
152.3647-2.23120.88483.9635-0.89611.02820.00250.10091.0013-0.0422-0.1384-1.6156-0.18110.7995-0.01370.0847-0.0408-0.07040.3636-0.01410.5944-3.0467-17.854341.2535
161.3463-0.53750.24051.8523-0.25510.4395-0.13720.06640.0487-0.1702-0.0090.0457-0.2949-0.089-0.0040.0204-0.04320.0040.07570.00910.003-30.5036-6.493619.0667
171.9018-0.33180.20941.7836-0.50773.27820.007-0.1242-0.13830.0614-0.0318-0.1010.1322-0.04610.0006-0.00870.0026-0.00330.060.0295-0.0157-27.7009-9.540219.7887
182.1792-0.0067-0.0551-0.2179-0.07840.50490.25270.0181-1.0282-0.62960.11660.0950.66660.0669-0.01540.2281-0.1006-0.09710.141-0.0290.1836-39.136-18.90155.5313
190.4534-0.3019-0.61660.9281-0.03280.3517-0.0203-0.1502-0.08760.0584-0.05930.13620.0713-0.1490.00050.0156-0.0468-0.01740.10070.02080.0579-37.3887-12.578619.571
200.2893-0.0208-0.12750.85770.22520.1832-0.1772-0.43750.08170.07730.08970.3541-0.7069-1.1453-0.0010.12340.0294-0.010.2924-0.00170.1318-40.7759-10.295121.8895
210.09360.0055-0.05060.3110.13920.1036-0.09840.0428-0.0896-0.30070.5406-1.1111-0.09630.23710.01070.7758-0.0540.23780.86060.26120.4904-4.8258-18.065124.5497
22-0.0393-0.0082-0.0218-0.00910.05640.11840.61460.0830.159-0.01590.18130.1891-0.4815-0.0225-0.00550.7824-0.14750.28261.04790.17950.5353-1.9941-3.618620.4753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 349:370)
2X-RAY DIFFRACTION2CHAIN A AND RESID 371:390)
3X-RAY DIFFRACTION3CHAIN A AND RESID 391:396)
4X-RAY DIFFRACTION4CHAIN A AND RESID 397:427)
5X-RAY DIFFRACTION5CHAIN A AND RESID 428:449)
6X-RAY DIFFRACTION6CHAIN A AND RESID 450:486)
7X-RAY DIFFRACTION7CHAIN A AND RESID 487:515)
8X-RAY DIFFRACTION8CHAIN A AND RESID 516:525)
9X-RAY DIFFRACTION9CHAIN A AND RESID 526:550)
10X-RAY DIFFRACTION10CHAIN A AND RESID 551:566)
11X-RAY DIFFRACTION11CHAIN B AND RESID 349:370)
12X-RAY DIFFRACTION12CHAIN B AND RESID 371:395)
13X-RAY DIFFRACTION13CHAIN B AND RESID 396:403)
14X-RAY DIFFRACTION14CHAIN B AND RESID 404:427)
15X-RAY DIFFRACTION15CHAIN B AND RESID 428:444)
16X-RAY DIFFRACTION16CHAIN B AND RESID 445:484)
17X-RAY DIFFRACTION17CHAIN B AND RESID 485:531)
18X-RAY DIFFRACTION18CHAIN B AND RESID 532:537)
19X-RAY DIFFRACTION19CHAIN B AND RESID 538:553)
20X-RAY DIFFRACTION20CHAIN B AND RESID 554:566)
21X-RAY DIFFRACTION21CHAIN C
22X-RAY DIFFRACTION22CHAIN D

+
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