[English] 日本語
Yorodumi
- PDB-3ikc: Structure of S67-27 in Complex with Kdo(2.8)-7-O-methyl-Kdo -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ikc
TitleStructure of S67-27 in Complex with Kdo(2.8)-7-O-methyl-Kdo
Components
  • Immunoglobulin heavy chain (IGG3)
  • Immunoglobulin light chain (IGG3)
KeywordsIMMUNE SYSTEM / antibody / Kdo / Chlamydia / LPS / Fab / carbohydrate
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBrooks, C.L. / Blackler, R.J. / Evans, S.V.
CitationJournal: Glycobiology / Year: 2010
Title: The role of CDR H3 in antibody recognition of a synthetic analog of a lipopolysaccharide antigen.
Authors: Brooks, C.L. / Blackler, R.J. / Sixta, G. / Kosma, P. / Muller-Loennies, S. / Brade, L. / Hirama, T. / Mackenzie, C.R. / Brade, H. / Evans, S.V.
History
DepositionAug 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_struct_conn_angle / 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.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Immunoglobulin light chain (IGG3)
B: Immunoglobulin heavy chain (IGG3)
C: Immunoglobulin light chain (IGG3)
D: Immunoglobulin heavy chain (IGG3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3168
Polymers97,2434
Non-polymers1,0744
Water5,999333
1
A: Immunoglobulin light chain (IGG3)
B: Immunoglobulin heavy chain (IGG3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1584
Polymers48,6212
Non-polymers5372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-15 kcal/mol
Surface area19270 Å2
MethodPISA
2
C: Immunoglobulin light chain (IGG3)
D: Immunoglobulin heavy chain (IGG3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1584
Polymers48,6212
Non-polymers5372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-15 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.240, 127.590, 155.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody Immunoglobulin light chain (IGG3)


Mass: 24090.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c
#2: Antibody Immunoglobulin heavy chain (IGG3)


Mass: 24530.635 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c
#3: Polysaccharide 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-8)-(1E)-prop-1-en-1-yl 3-deoxy-7-O-methyl-alpha- ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-8)-(1E)-prop-1-en-1-yl 3-deoxy-7-O-methyl-alpha-D-manno-oct-2-ulopyranosidonic acid


Type: oligosaccharide / Mass: 512.459 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[Aad1122h-2a_2-6_2*OC=^ECC_7*OC][Aad1122h-2a_2-6]/1-2/a8-b2WURCSPDB2Glycan 1.1.0
[][propyl]{[(1+2)][a-D-Kdop7Me]{[(8+2)][a-D-Kdop]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, MgCl2, pH 8.5, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 27, 2009 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→19.96 Å / Num. obs: 26726 / % possible obs: 91.7 % / Redundancy: 3.91 % / Rmerge(I) obs: 0.089 / Χ2: 0.96 / Net I/σ(I): 8.5 / Scaling rejects: 790
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.6-2.693.860.263.51074127771.1297.8
2.69-2.83.870.23241075627731.197.3
2.8-2.933.820.2074.81064727781.196.5
2.93-3.083.830.1735.41068627871.0496
3.08-3.273.860.1456.71042626871.0394.2
3.27-3.523.930.09591033826140.8889.9
3.52-3.883.980.07810.21017925320.8786.5
3.88-4.434.070.06712.31007824470.8584.5
4.43-5.564.070.05815.61029424790.8283.4
5.56-19.963.830.05913.81108428520.891.6

-
Processing

Software
NameVersionClassificationNB
d*TREK9.7 W8RSSIdata processing
PHENIX1.4_4refinement
PDB_EXTRACT3.005data extraction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1Q9W

1q9w


Resolution: 2.6→19.96 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 1.16 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.291 1348 5.05 %
Rwork0.235 --
obs0.238 26678 91.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.446 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 102.67 Å2 / Biso mean: 34.997 Å2 / Biso min: 12.77 Å2
Baniso -1Baniso -2Baniso -3
1-13.725 Å2-0 Å20 Å2
2---10.764 Å20 Å2
3----2.961 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6776 0 72 333 7181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047014
X-RAY DIFFRACTIONf_angle_d0.9019531
X-RAY DIFFRACTIONf_chiral_restr0.0561079
X-RAY DIFFRACTIONf_plane_restr0.0041198
X-RAY DIFFRACTIONf_dihedral_angle_d17.1032503
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.6930.3821490.2952624277398
2.693-2.80.3541450.2852623276897
2.8-2.9270.3841340.2732641277596
2.927-3.0810.3691510.2682635278696
3.081-3.2730.3161340.2522552268694
3.273-3.5250.2831290.2212483261290
3.525-3.8770.2791240.2162405252986
3.877-4.4330.2271270.1882317244484
4.433-5.5650.1781230.1682351247483
5.565-19.9640.2641320.2082699283191

+
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