[English] 日本語
Yorodumi
- PDB-6s2y: Water-soluble Chlorophyll Protein (WSCP) from Lepidium virginicum... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s2y
TitleWater-soluble Chlorophyll Protein (WSCP) from Lepidium virginicum with Chlorophyll-b
ComponentsWater-soluble chlorophyll protein
KeywordsPLANT PROTEIN / Tetramer / Plant / Lepidium virginicum / Chlorophyll / Water-soluble Chlorophyll Protein / Photooxidation / Chlorophyll Carrier
Function / homology
Function and homology information


endopeptidase inhibitor activity
Similarity search - Function
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
CHLOROPHYLL B / Water-soluble chlorophyll protein
Similarity search - Component
Biological speciesLepidium virginicum (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAgostini, A. / Meneghin, E. / Gewehr, L. / Pedron, D. / Palm, D.M. / Carbonera, D. / Paulsen, H. / Jaenicke, E. / Collini, E.
Funding support Germany, Italy, 2items
OrganizationGrant numberCountry
German Research FoundationPa 324/10-1 Germany
Italian Ministry of EducationPRIN 2015 no. 2015XBZ5YA Italy
CitationJournal: Sci Rep / Year: 2019
Title: How water-mediated hydrogen bonds affect chlorophyll a/b selectivity in Water-Soluble Chlorophyll Protein.
Authors: Agostini, A. / Meneghin, E. / Gewehr, L. / Pedron, D. / Palm, D.M. / Carbonera, D. / Paulsen, H. / Jaenicke, E. / Collini, E.
History
DepositionJun 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / refine / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Water-soluble chlorophyll protein
B: Water-soluble chlorophyll protein
C: Water-soluble chlorophyll protein
D: Water-soluble chlorophyll protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9968
Polymers78,3664
Non-polymers3,6304
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, The structure is homologous to structure 2DRE only difference being the ligand (CHL instead of CLA)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11730 Å2
ΔGint-94 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.310, 82.900, 122.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA4 - 1794 - 179
21BB4 - 1794 - 179
12AA5 - 1795 - 179
22CC5 - 1795 - 179
13AA5 - 1795 - 179
23DD5 - 1795 - 179
14BB5 - 1795 - 179
24CC5 - 1795 - 179
15BB5 - 1795 - 179
25DD5 - 1795 - 179
16CC5 - 1795 - 179
26DD5 - 1795 - 179

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Water-soluble chlorophyll protein


Mass: 19591.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lepidium virginicum (plant) / Tissue: Leaf / Gene: WSCP1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O04797
#2: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Na/K Phosphate, 3.0M Ammonium sulfate, 4.7% Sucrose

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 4, 2018 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→19.63 Å / Num. obs: 33323 / % possible obs: 98.7 % / Redundancy: 4.62 % / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.31
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.76 % / Mean I/σ(I) obs: 3.03 / Num. unique obs: 2427 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSVERSION Mar 15, 2019data reduction
XSCALEVERSION Mar 15, 2019data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DRE

2dre


Resolution: 2.3→19.63 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.408 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2766 1667 5 %RANDOM
Rwork0.2434 ---
obs0.2451 31655 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.37 Å2 / Biso mean: 43.068 Å2 / Biso min: 11.98 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.3→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4914 0 264 130 5308
Biso mean--31.25 35.28 -
Num. residues----639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125328
X-RAY DIFFRACTIONr_angle_refined_deg2.3841.7297297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5045621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09823.801221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74815813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9131519
X-RAY DIFFRACTIONr_chiral_restr0.0940.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024018
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A43780.13
12B43780.13
21A44800.11
22C44800.11
31A44400.11
32D44400.11
41B44420.12
42C44420.12
51B43730.13
52D43730.13
61C47050.1
62D47050.1
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 120 -
Rwork0.305 2276 -
all-2396 -
obs--99.71 %

+
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