[English] 日本語
Yorodumi
- PDB-4jg1: Structure of phosphoserine/threonine (pSTAb) scaffold bound to pT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jg1
TitleStructure of phosphoserine/threonine (pSTAb) scaffold bound to pThr peptide
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • Phosphopeptide
KeywordsIMMUNE SYSTEM / immmunoglobulin domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PROPANOIC ACID
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsKoerber, J.T. / Thomsen, N.D. / Hannigan, B.T. / Degrado, W.F. / Wells, J.A.
CitationJournal: Nat.Biotechnol. / Year: 2013
Title: Nature-inspired design of motif-specific antibody scaffolds.
Authors: Koerber, J.T. / Thomsen, N.D. / Hannigan, B.T. / Degrado, W.F. / Wells, J.A.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Mar 26, 2014Group: Source and taxonomy
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Fab light chain
H: Fab heavy chain
P: Phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5844
Polymers49,5103
Non-polymers741
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-33 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.807, 95.591, 119.817
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

-
Components

#1: Antibody Fab light chain / Fragment antigen-binding


Mass: 23303.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): C43 PRO+
#2: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 24790.717 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): C43 PRO+
#3: Protein/peptide Phosphopeptide /


Mass: 1415.465 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-PPI / PROPANOIC ACID / Propionic acid


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG1500, 0.1M PCB, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 278K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2012
RadiationMonochromator: DOUBLE FLAT CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 72575 / Num. obs: 72575 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.065 / Χ2: 1.075 / Net I/σ(I): 13.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.612.90.50864191.063188.1
1.61-1.673.70.40769631.086195.2
1.67-1.755.20.32672081.085198.2
1.75-1.845.90.22272421.087199
1.84-1.9560.14473021.087199.4
1.95-2.160.09673441.057199.6
2.1-2.326.20.07273711.049199.8
2.32-2.656.40.0674121.099199.9
2.65-3.346.60.05875041.0931100
3.34-506.70.03678101.046199.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
ELVESrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 3N9G, 2GCY

3n9g

2gcy


Resolution: 1.55→41.143 Å / Occupancy max: 1 / Occupancy min: 0.08 / FOM work R set: 0.9044 / SU ML: 0.11 / σ(F): 1.36 / Phase error: 16.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1738 3659 5.05 %RANDOM
Rwork0.1507 ---
obs0.1518 72503 97.84 %-
all-72503 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.37 Å2 / Biso mean: 21.011 Å2 / Biso min: 8.14 Å2
Refinement stepCycle: LAST / Resolution: 1.55→41.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 5 621 4017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013744
X-RAY DIFFRACTIONf_angle_d1.3535162
X-RAY DIFFRACTIONf_chiral_restr0.083601
X-RAY DIFFRACTIONf_plane_restr0.007668
X-RAY DIFFRACTIONf_dihedral_angle_d13.1741430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5486-1.5690.24851240.24022120224480
1.569-1.59040.2561090.2242411252090
1.5904-1.61320.26041260.21262502262893
1.6132-1.63730.22711400.19572473261394
1.6373-1.66280.22291270.19242624275197
1.6628-1.69010.19561280.18622636276498
1.6901-1.71920.20211470.17372588273598
1.7192-1.75050.20431240.17112705282999
1.7505-1.78420.2231260.15742633275999
1.7842-1.82060.1761510.15812656280799
1.8206-1.86020.18171620.1482612277499
1.8602-1.90350.14961420.150127162858100
1.9035-1.95110.16891480.13932626277499
1.9511-2.00380.15921480.13742678282699
2.0038-2.06280.17361320.136626992831100
2.0628-2.12930.15261330.14226982831100
2.1293-2.20540.16431500.135726802830100
2.2054-2.29370.16041830.141326712854100
2.2937-2.39810.16921270.14327242851100
2.3981-2.52450.17581470.143526952842100
2.5245-2.68270.17991460.148127082854100
2.6827-2.88980.17541550.1527432898100
2.8898-3.18050.16781530.155227452898100
3.1805-3.64050.17711390.142827682907100
3.6405-4.58560.15291400.125727952935100
4.5856-41.15780.15521520.159529383090100
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)
10.81510.29-0.46130.9666-0.82441.3679-0.039-0.0576-0.0281-0.0355-0.0087-0.03360.07820.1583-00.1120.00480.00450.135-0.00510.125827.20331.889248.0527
20.33620.15640.6059-0.0250.29611.67490.0111-0.0129-0.00020.03-0.0023-0.03050.00910.089900.1220.00080.00150.108-0.00960.133519.320734.959713.3892
30.67780.59510.01571.6550.61230.9614-0.011-0.0190.0132-0.06390.0517-0.0485-0.06040.00870.00020.12250.0063-0.00950.11830.00460.128714.255140.261151.7879
40.87470.4953-0.42430.9481-0.29922.09540.0278-0.0256-0.0239-0.0089-0.01090.0540.0972-0.1058-00.1062-0.0021-0.00070.1233-0.01080.12340.177726.06822.2984
50.83040.0163-0.39410.53090.05510.19620.11830.76630.0941-0.4398-0.07210.2011-0.1821-0.76170.01910.19610.0144-0.01510.23320.0270.15555.090234.5624-1.4716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain H and resseq 125:238)H125 - 238
2X-RAY DIFFRACTION2(chain H and resseq 1:124)H1 - 124
3X-RAY DIFFRACTION3(chain L and resseq 109:214)L109 - 214
4X-RAY DIFFRACTION4(chain L and resseq 1:108)L1 - 108
5X-RAY DIFFRACTION5(chain P and resseq 1:9)P1 - 9

+
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