[English] 日本語
Yorodumi
- PDB-7o30: Crystal structure of the anti-PAS Fab 1.1 in complex with its epi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o30
TitleCrystal structure of the anti-PAS Fab 1.1 in complex with its epitope peptide
Components
  • PAS#1 epitope peptide
  • anti-PAS Fab 1.1 chimeric heavy chain
  • anti-PAS Fab 1.1 chimeric light chain
KeywordsIMMUNE SYSTEM / antibody / disordered protein antigen / PAS polypeptide / protein engineering
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsSchilz, J. / Schiefner, A. / Skerra, A.
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Molecular recognition of structurally disordered Pro/Ala-rich sequences (PAS) by antibodies involves an Ala residue at the hot spot of the epitope.
Authors: Schilz, J. / Binder, U. / Friedrich, L. / Gebauer, M. / Lutz, C. / Schlapschy, M. / Schiefner, A. / Skerra, A.
History
DepositionApr 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 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
L: anti-PAS Fab 1.1 chimeric light chain
H: anti-PAS Fab 1.1 chimeric heavy chain
P: PAS#1 epitope peptide
A: anti-PAS Fab 1.1 chimeric light chain
B: anti-PAS Fab 1.1 chimeric heavy chain
Q: PAS#1 epitope peptide


Theoretical massNumber of molelcules
Total (without water)99,1296
Polymers99,1296
Non-polymers00
Water95553
1
L: anti-PAS Fab 1.1 chimeric light chain
H: anti-PAS Fab 1.1 chimeric heavy chain
P: PAS#1 epitope peptide


Theoretical massNumber of molelcules
Total (without water)49,5643
Polymers49,5643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-36 kcal/mol
Surface area20330 Å2
MethodPISA
2
A: anti-PAS Fab 1.1 chimeric light chain
B: anti-PAS Fab 1.1 chimeric heavy chain
Q: PAS#1 epitope peptide


Theoretical massNumber of molelcules
Total (without water)49,5643
Polymers49,5643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-33 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.615, 102.615, 199.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21A
12H
22B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPCYSCYSLA1 - 2181 - 218
21ASPASPCYSCYSAD1 - 2181 - 218
12GLUGLUGLUGLUHB1 - 2191 - 219
22GLUGLUGLUGLUBE1 - 2191 - 219

NCS ensembles :
ID
1
2

-
Components

#1: Antibody anti-PAS Fab 1.1 chimeric light chain


Mass: 23977.631 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody anti-PAS Fab 1.1 chimeric heavy chain


Mass: 24723.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide PAS#1 epitope peptide


Mass: 862.925 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: PCA in the peptide sequence is the residue code for pyroglutamic acid
Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% (w/v) PEG 3350 100 mM HEPES pH 7.5 200 mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 27, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.65→34.13 Å / Num. obs: 30855 / % possible obs: 96.9 % / Redundancy: 22.197 % / Biso Wilson estimate: 63.305 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.112 / Χ2: 0.87 / Net I/σ(I): 24.34 / Num. measured all: 684889 / Scaling rejects: 1117
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.7518.2561.6312.1355755327430540.7571.67593.3
2.75-2.8520.371.23.1354470286326740.8691.22993.4
2.85-322.2070.8674.6975350355733930.9390.88695.4
3-3.522.8110.33211.74175095802476760.9910.33995.7
3.5-421.6720.13626.5597588454445030.9980.13999.1
4-624.260.06549.19159998661065950.9990.06699.8
6-822.130.0554.47370021672167210.051100
8-1023.8370.03374.251444560660610.034100
10-34.1322.2670.02973.391518670868210.02996.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.04 Å34.48 Å
Translation3.04 Å34.48 Å

-
Processing

Software
NameVersionClassification
XDS16.8.2013data reduction
XSCALEMar 15, 2019data scaling
PHASER2.8.3phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O2Z

7o2z


Resolution: 2.65→34.13 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.91 / SU B: 15.506 / SU ML: 0.302 / SU R Cruickshank DPI: 1.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.105 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 1498 4.9 %RANDOM
Rwork0.22 ---
obs0.2223 29357 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 169.14 Å2 / Biso mean: 67.467 Å2 / Biso min: 30.91 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å20 Å20 Å2
2---2.79 Å20 Å2
3---5.58 Å2
Refinement stepCycle: final / Resolution: 2.65→34.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6784 0 0 53 6837
Biso mean---46.21 -
Num. residues----892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136957
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176208
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.6459474
X-RAY DIFFRACTIONr_angle_other_deg1.0871.5714522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8645884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26323.087298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.561151102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4541526
X-RAY DIFFRACTIONr_chiral_restr0.0450.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027790
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021384
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11L60860.1
12A60860.1
21H60200.08
22B60200.08
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 103 -
Rwork0.394 2031 -
all-2134 -
obs--92.5 %

+
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