[English] 日本語
Yorodumi
- PDB-7c2p: Structure of Egk Peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c2p
TitleStructure of Egk Peptide
ComponentsPlant defensing Egk
KeywordsPROTEIN BINDING / Plant Defensin
Biological speciesElaeis guineensis (African oil palm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEl Sahili, A.
CitationJournal: Acs Pharmacol Transl Sci / Year: 2020
Title: Modulation of Lymphocyte Potassium Channel KV1.3 by Membrane-Penetrating, Joint-Targeting Immunomodulatory Plant Defensin.
Authors: Ong, S.T. / Bajaj, S. / Tanner, M.R. / Chang, S.C. / Krishnarjuna, B. / Ng, X.R. / Morales, R.A.V. / Chen, M.W. / Luo, D. / Patel, D. / Yasmin, S. / Ng, J.J.H. / Zhuang, Z. / Nguyen, H.M. / ...Authors: Ong, S.T. / Bajaj, S. / Tanner, M.R. / Chang, S.C. / Krishnarjuna, B. / Ng, X.R. / Morales, R.A.V. / Chen, M.W. / Luo, D. / Patel, D. / Yasmin, S. / Ng, J.J.H. / Zhuang, Z. / Nguyen, H.M. / El Sahili, A. / Lescar, J. / Patil, R. / Charman, S.A. / Robins, E.G. / Goggi, J.L. / Tan, P.W. / Sadasivam, P. / Ramasamy, B. / Hartimath, S.V. / Dhawan, V. / Bednenko, J. / Colussi, P. / Wulff, H. / Pennington, M.W. / Kuyucak, S. / Norton, R.S. / Beeton, C. / Chandy, K.G.
History
DepositionMay 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Plant defensing Egk
B: Plant defensing Egk
C: Plant defensing Egk
D: Plant defensing Egk


Theoretical massNumber of molelcules
Total (without water)21,4054
Polymers21,4054
Non-polymers00
Water43224
1
A: Plant defensing Egk


Theoretical massNumber of molelcules
Total (without water)5,3511
Polymers5,3511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plant defensing Egk


Theoretical massNumber of molelcules
Total (without water)5,3511
Polymers5,3511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Plant defensing Egk


Theoretical massNumber of molelcules
Total (without water)5,3511
Polymers5,3511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Plant defensing Egk


Theoretical massNumber of molelcules
Total (without water)5,3511
Polymers5,3511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.84, 37.92, 54.77
Angle α, β, γ (deg.)83.76, 78.35, 70.22
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein/peptide
Plant defensing Egk


Mass: 5351.280 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elaeis guineensis (African oil palm) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium tartrate dibasic dehydrate, 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.000034 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000034 Å / Relative weight: 1
ReflectionResolution: 2.1→65 Å / Num. obs: 9535 / % possible obs: 88.3 % / Redundancy: 1.7 % / CC1/2: 0.902 / Rmerge(I) obs: 0.16 / Net I/σ(I): 3.11
Reflection shellResolution: 2.1→2.22 Å / Num. unique obs: 1392 / CC1/2: 0.67

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UJ0

4uj0


Resolution: 2.1→35.65 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.9 / SU R Cruickshank DPI: 0.326 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.312 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.226
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 476 -RANDOM
Rwork0.2295 ---
obs0.2311 9514 88.7 %-
Displacement parametersBiso mean: 52.06 Å2
Baniso -1Baniso -2Baniso -3
1--3.8592 Å22.9341 Å20.0943 Å2
2--1.3433 Å20.8145 Å2
3---2.5159 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.1→35.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1472 0 0 24 1496
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081528HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.892029HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d567SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes263HARMONIC5
X-RAY DIFFRACTIONt_it1528HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion181SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact982SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion17.35
LS refinement shellResolution: 2.1→2.13 Å
RfactorNum. reflection% reflection
Rfree0.3273 21 -
Rwork0.2859 --
obs0.2882 414 82.94 %
Refinement TLS params.

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)
13.9477-0.1555-0.62626.1829-0.95190.42060.24310.1838-0.14280.1838-0.21810.1019-0.14280.1019-0.025-0.13490.0667-0.0852-0.472-0.0144-0.488931.201856.3775-8.9333
23.11281.0137-0.33686.1003-1.29161.310.13950.1425-0.22470.1425-0.2744-0.0507-0.2247-0.05070.1348-0.14480.10790.0066-0.49450.0119-0.472323.891639.3943-9.2669
35.0616-3.31912.80049.78520.0254-0.7671-0.1350.00060.25520.00060.20030.0350.25520.035-0.0653-0.20940.12150.0155-0.45980.0285-0.406225.493456.5206-36.1229
43.336-2.55520.04188.3507-0.6947-0.0683-0.2091-0.0438-0.3142-0.04380.0269-0.0608-0.3142-0.06080.1822-0.22460.1409-0.0133-0.4139-0.0644-0.414232.740238.7264-36.0847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

+
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://pdbjlvh1.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