[English] 日本語
Yorodumi
- PDB-5l88: AFAMIN ANTIBODY FRAGMENT, N14 FAB, L1- GLYCOSILATED, CRYSTAL FORM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l88
TitleAFAMIN ANTIBODY FRAGMENT, N14 FAB, L1- GLYCOSILATED, CRYSTAL FORM I, non-parsimonious model
Components(Anti-afamin antibody N14, Fab fragment, ...) x 2
KeywordsIMMUNE SYSTEM / Afamin antibody / Fab Fragment / IgG1-kappa / light chain glycosilation
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsRupp, B. / Naschberger, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP28395-B26 Austria
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: The N14 anti-afamin antibody Fab: a rare VL1 CDR glycosylation, crystallographic re-sequencing, molecular plasticity and conservative versus enthusiastic modelling.
Authors: Naschberger, A. / Furnrohr, B.G. / Lenac Rovis, T. / Malic, S. / Scheffzek, K. / Dieplinger, H. / Rupp, B.
History
DepositionJun 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Data collection
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Dec 21, 2016Group: Database references
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / software / struct_asym / struct_conn / struct_conn_type / 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 / _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 / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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 / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Anti-afamin antibody N14, Fab fragment, heavy chain
L: Anti-afamin antibody N14, Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,20618
Polymers47,3452
Non-polymers2,86116
Water4,540252
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint27 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.782, 69.249, 87.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Antibody , 2 types, 2 molecules HL

#1: Antibody Anti-afamin antibody N14, Fab fragment, heavy chain


Mass: 23686.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#2: Antibody Anti-afamin antibody N14, Fab fragment, light chain


Mass: 23658.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C

-
Sugars , 1 types, 1 molecules

#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

-
Non-polymers , 7 types, 267 molecules

#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#6: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#9: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.9 %
Description: Block-shaped crystals with sharp edges (0.15 x 0.15 x 0.3 mm)
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.8
Details: 200nL Fab 10mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl plus 200nL 30%w/v PEG 1k, 200mM KF, pH 5.8)
Temp details: Air conditioned room

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2015 / Details: Torroidal focussing mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→54.37 Å / Num. obs: 34249 / % possible obs: 99.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 36.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Net I/σ(I): 10
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.4 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
autoPROCdata collection
autoPROCdata scaling
XDSdata reduction
SCALAdata scaling
BALBESphasing
Cootmodel building
WARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IL1

1il1


Resolution: 1.88→47.38 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.297 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21145 1659 4.9 %RANDOM
Rwork0.17003 ---
obs0.17212 32346 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.307 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å2-0 Å20 Å2
2---0.54 Å2-0 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.88→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 189 252 3741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023691
X-RAY DIFFRACTIONr_bond_other_d0.0020.023384
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9824982
X-RAY DIFFRACTIONr_angle_other_deg0.86537923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4365.021475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17324.662133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57915.043579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.755159
X-RAY DIFFRACTIONr_chiral_restr0.0810.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214000
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02771
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_it2.1025.5741782
X-RAY DIFFRACTIONr_mcbond_other2.0895.5651781
X-RAY DIFFRACTIONr_mcangle_it3.13610.3812240
X-RAY DIFFRACTIONr_mcangle_other3.14310.3932241
X-RAY DIFFRACTIONr_scbond_it3.1716.8261909
X-RAY DIFFRACTIONr_scbond_other3.1696.8261909
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.64712.0772732
X-RAY DIFFRACTIONr_long_range_B_refined6.72327.1824013
X-RAY DIFFRACTIONr_long_range_B_other6.72227.1944014
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 122 -
Rwork0.326 2299 -
obs--96.69 %
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)
10.87540.07920.34910.1890.0530.63970.0680.0373-0.04760.1236-0.0176-0.0570.0428-0.0498-0.05030.0992-0.0208-0.04790.04560.02770.03263.99182.17722.7118
20.05940.1568-0.12331.29840.02110.61810.0336-0.02780.0222-0.01540.03780.02540.0230.086-0.07150.10240.0031-0.00640.0692-0.02720.015623.406932.121532.3033
30.04680.0532-0.05570.5421-0.00050.6540.01260.04590.01280.01380.0198-0.04810.0434-0.0309-0.03240.03830.01030.00920.0932-0.01440.03336.644411.2692.2427
40.44530.07680.20650.0433-0.06620.9680.0362-0.0062-0.02610.01640.02170.0002-0.03290.1153-0.05790.070.0202-0.00830.1159-0.02440.012229.46726.517219.2131
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 107
2X-RAY DIFFRACTION1L301 - 302
3X-RAY DIFFRACTION2L108 - 213
4X-RAY DIFFRACTION3H1 - 113
5X-RAY DIFFRACTION4H114 - 214

+
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