[English] 日本語
Yorodumi
- PDB-3c6s: Crystal structure of Fab F22-4 in complex with a Shigella flexner... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c6s
TitleCrystal structure of Fab F22-4 in complex with a Shigella flexneri 2a O-Ag pentadecasaccharide
Components
  • Fab F22-4 heavy chain
  • Fab F22-4 light chain
KeywordsIMMUNE SYSTEM / O-antigen / LPS / Shigella flexneri / antibody complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PALLADIUM ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSaul, F.A. / Vulliez-le-Normand, B. / Bentley, G.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structures of synthetic O-antigen fragments from serotype 2a Shigella flexneri in complex with a protective monoclonal antibody
Authors: Vulliez-Le Normand, B. / Saul, F.A. / Phalipon, A. / Belot, F. / Guerreiro, C. / Mulard, L.A. / Bentley, G.A.
History
DepositionFeb 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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 / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_ref_seq / 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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conn.conn_type_id / _struct_conn.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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fab F22-4 light chain
B: Fab F22-4 heavy chain
C: Fab F22-4 light chain
D: Fab F22-4 heavy chain
E: Fab F22-4 light chain
F: Fab F22-4 heavy chain
G: Fab F22-4 light chain
H: Fab F22-4 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,29913
Polymers191,1068
Non-polymers7,1935
Water38,2642124
1
A: Fab F22-4 light chain
B: Fab F22-4 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6544
Polymers47,7762
Non-polymers1,8782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint21 kcal/mol
Surface area19330 Å2
MethodPISA
2
C: Fab F22-4 light chain
D: Fab F22-4 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5483
Polymers47,7762
Non-polymers1,7721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint24 kcal/mol
Surface area19360 Å2
MethodPISA
3
E: Fab F22-4 light chain
F: Fab F22-4 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5483
Polymers47,7762
Non-polymers1,7721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint25 kcal/mol
Surface area19170 Å2
MethodPISA
4
G: Fab F22-4 light chain
H: Fab F22-4 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5483
Polymers47,7762
Non-polymers1,7721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint26 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.860, 137.150, 109.380
Angle α, β, γ (deg.)90.00, 94.97, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody
Fab F22-4 light chain


Mass: 24141.777 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c
#2: Antibody
Fab F22-4 heavy chain


Mass: 23634.598 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c
#3: Polysaccharide
alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose-(1-3)-[alpha-D-glucopyranose-(1-4)]alpha-L- ...alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose-(1-3)-[alpha-D-glucopyranose-(1-4)]alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose-(1-3)-[alpha-D-glucopyranose-(1-4)]alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-L-rhamnopyranose


Type: oligosaccharide / Mass: 1771.668 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-2LRhapa1-3[DGlcpa1-4]LRhapa1-3DGlcpNAcb1-2LRhapa1-2LRhapa1-3[DGlcpa1-4]LRhapa1-3DGlcpNAcb1-2LRhapa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,11,10/[a2211m-1a_1-5][a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5]/1-2-1-1-1-2-1-1-1-3-3/a2-b1_b3-c1_c3-d1_c4-k1_d2-e1_e2-f1_f3-g1_g3-h1_g4-j1_h2-i1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Rhap]{[(2+1)][b-D-GlcpNAc]{[(3+1)][a-L-Rhap]{[(3+1)][a-L-Rhap]{[(2+1)][a-L-Rhap]{[(2+1)][b-D-GlcpNAc]{[(3+1)][a-L-Rhap]{[(3+1)][a-L-Rhap]{[(2+1)][a-L-Rhap]{}}[(4+1)][a-D-Glcp]{}}}}}[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-PD / PALLADIUM ION


Mass: 106.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pd
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2124 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsPENTADECASACCHARIDE CORRESPONDING TO THREE SHIGELLA FLEXNERI SEROTYPE 2A O-ANTIGEN REPEATING UNITS. ...PENTADECASACCHARIDE CORRESPONDING TO THREE SHIGELLA FLEXNERI SEROTYPE 2A O-ANTIGEN REPEATING UNITS. FOUR SUGAR RESIDUES AT THE REDUCING END OF EACH PENTADECASACCHARIDE WERE NOT DETERMINED IN THE STRUCTURE DUE TO LACK OF ELECTRON DENSITY.
Sequence detailsTHE SEQUENCE DATABASE FOR CHAINS A,C,E,G RESIDUES 1-107 IS CAH04481.2, AND FOR CHAINS B,D,F,H ...THE SEQUENCE DATABASE FOR CHAINS A,C,E,G RESIDUES 1-107 IS CAH04481.2, AND FOR CHAINS B,D,F,H RESIDUES 1-113 IS CAH04480.1. RESIDUE NUMBERING OF ANTIBODY VARIABLE REGIONS FOLLOWS THE KABAT CONVENTION (E.A. KABAT, T.T. WU, H.M. PERRY, K.S. GOTTESMAN, C. FOELLER. SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 5TH ED. (1991). NIH PUBLICATION NO. 91-3242, NATIONAL INSTITUTES OF HEALTH, BETHESDA, MD). DISCREPANCIES BETWEEN THE DATABASE SEQUENCE CAH04481.2 AND THIS PDB ENTRY OCCUR AT POSITIONS ASP 1, ILE 2, ALA 7, ALA 8, AND PHE 9 (CHAINS A,C,E,G), AND BETWEEN DATABASE SEQUENCE CAH04480.1 AND THIS ENTRY AT POSITION VAL 4 (CHAINS B,D,F, H). THESE N-TERMINAL SEQUENCE DISCREPANCIES ARE DUE TO THE PRIMERS USED FOR NUCLEOTIDE SEQUENCE DETERMINATION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 25% PEG 5000 MME, 0.2M Li2SO4, 0.1M Tris, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2006 / Details: bent mirror
RadiationMonochromator: Diamond(111), Ge(220) toroidal focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→45.74 Å / Num. all: 179612 / Num. obs: 179612 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 16.86 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 1 / Num. unique all: 25673 / Rsym value: 0.668 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
ADSCQuantumdata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3C5S

3c5s


Resolution: 1.8→44.79 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.909 / SU B: 3.694 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25109 2670 1.5 %RANDOM
Rwork0.19141 ---
all0.1923 176903 --
obs0.1923 176903 99.11 %-
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: 18.781 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å2-0.02 Å2
2--2.2 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13125 0 481 2124 15730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02214020
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212150
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.99519185
X-RAY DIFFRACTIONr_angle_other_deg0.804328335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87651700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10223.895534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.173152180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0021561
X-RAY DIFFRACTIONr_chiral_restr0.0910.22288
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214952
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022681
X-RAY DIFFRACTIONr_nbd_refined0.1990.22399
X-RAY DIFFRACTIONr_nbd_other0.1960.212588
X-RAY DIFFRACTIONr_nbtor_refined0.1810.26792
X-RAY DIFFRACTIONr_nbtor_other0.0870.28167
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.21708
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0180.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.280.293
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1510.22
X-RAY DIFFRACTIONr_mcbond_it1.578210762
X-RAY DIFFRACTIONr_mcbond_other0.32223453
X-RAY DIFFRACTIONr_mcangle_it1.957313819
X-RAY DIFFRACTIONr_scbond_it2.00436531
X-RAY DIFFRACTIONr_scangle_it2.71545357
LS refinement shellResolution: 1.8→1.823 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.354 97 -
Rwork0.281 6431 -
obs-6528 97.06 %

+
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