[English] 日本語
Yorodumi
- PDB-5dju: Crystal structure of LOV2 (C450A) domain in complex with Zdk3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dju
TitleCrystal structure of LOV2 (C450A) domain in complex with Zdk3
Components
  • Engineered protein, Zdk3 affibody
  • NPH1-2
KeywordsSIGNALING PROTEIN / Protein binding / Protein engineering / Photoswitch / Light-induced signal transduction / LOV2 / Affibody / Complex
Function / homology
Function and homology information


blue light photoreceptor activity / protein kinase activity / protein phosphorylation / ATP binding
Similarity search - Function
Immunoglobulin FC, subunit C / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. ...Immunoglobulin FC, subunit C / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / PAS domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NPH1-2
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Avena sativa (oats)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTarnawski, M. / Wang, H. / Yumerefendi, H. / Hahn, K.M. / Schlichting, I.
CitationJournal: Nat.Methods / Year: 2016
Title: LOVTRAP: an optogenetic system for photoinduced protein dissociation.
Authors: Wang, H. / Vilela, M. / Winkler, A. / Tarnawski, M. / Schlichting, I. / Yumerefendi, H. / Kuhlman, B. / Liu, R. / Danuser, G. / Hahn, K.M.
History
DepositionSep 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Jan 10, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Engineered protein, Zdk3 affibody
A: NPH1-2
D: Engineered protein, Zdk3 affibody
C: NPH1-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,00111
Polymers46,9114
Non-polymers1,0907
Water3,945219
1
B: Engineered protein, Zdk3 affibody
A: NPH1-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0186
Polymers23,4552
Non-polymers5634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-39 kcal/mol
Surface area10080 Å2
MethodPISA
2
D: Engineered protein, Zdk3 affibody
C: NPH1-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9835
Polymers23,4552
Non-polymers5273
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-43 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.240, 74.500, 81.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Engineered protein, Zdk3 affibody


Mass: 6823.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein NPH1-2


Mass: 16631.729 Da / Num. of mol.: 2 / Fragment: UNP residues 404-546 / Mutation: C450A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Avena sativa (oats) / Gene: NPH1-2 / Production host: Escherichia coli (E. coli) / References: UniProt: O49004
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Mutation: C450A
Source method: isolated from a genetically manipulated source
Formula: C17H21N4O9P / Source: (gene. exp.) Avena sativa (oats) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M citric acid pH 4.0, 1.0 M lithium chloride, 18% (w/v) PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00005 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 26342 / % possible obs: 96.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 6.7
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 2.1 / % possible all: 88.3

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WKQ and a homology model based on 1Q2N

2wkq

1q2n


Resolution: 2.1→44.252 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2582 1318 5 %
Rwork0.2049 --
obs0.2075 26338 96.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→44.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 5 219 3516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083358
X-RAY DIFFRACTIONf_angle_d1.0734553
X-RAY DIFFRACTIONf_dihedral_angle_d15.0621269
X-RAY DIFFRACTIONf_chiral_restr0.046499
X-RAY DIFFRACTIONf_plane_restr0.006591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.18410.3441310.26622471X-RAY DIFFRACTION87
2.1841-2.28350.33031440.23832745X-RAY DIFFRACTION98
2.2835-2.40390.29561490.22982823X-RAY DIFFRACTION99
2.4039-2.55450.28281460.23072775X-RAY DIFFRACTION99
2.5545-2.75170.26491470.20942804X-RAY DIFFRACTION99
2.7517-3.02850.27981490.21272816X-RAY DIFFRACTION98
3.0285-3.46660.25171470.2022800X-RAY DIFFRACTION98
3.4666-4.36690.22031490.17782834X-RAY DIFFRACTION98
4.3669-44.26210.2321560.19162952X-RAY DIFFRACTION97
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)
13.39384.22782.65016.1411.86695.2823-0.00740.87180.4575-0.36780.20630.2827-0.10650.1907-0.31610.25680.07920.04910.3710.05210.2936-1.596313.8325-10.3308
22.3935-0.30920.05582.56690.59954.17930.0728-0.09310.40440.11540.0401-0.0497-0.14890.3518-0.07670.162-0.02360.04080.26670.0090.311-2.850514.68911.7736
32.3021-0.20460.424.12940.80652.30270.10270.0136-0.1456-0.11180.0067-0.15630.24260.2883-0.09630.20550.0115-0.03390.25180.02530.22423.2976-5.9501-8.0621
47.4405-5.8262-5.05175.01184.59824.5949-0.4517-0.1852-0.00850.87690.8062-0.35390.63830.5856-0.2550.33260.0115-0.1060.41310.0090.347214.3678-7.26760.2772
54.59664.2454.81543.92074.46566.0171-0.22060.15710.76550.14570.14020.5419-0.4252-0.04150.13220.21660.03560.03190.25870.00540.4394-16.7725-8.519-35.8718
60.3435-0.22140.372.737-0.10042.4767-0.08890.10180.04760.03750.1025-0.1302-0.0006-0.0216-0.01560.19260.0311-0.01290.2612-0.05660.369-15.7134-20.4839-36.8694
72.02610.46560.69721.3684-0.2153.790.0783-0.29480.01060.1140.02340.1511-0.1302-0.1193-0.10360.2153-0.01480.01840.2949-0.06960.347-22.3436-10.8187-16.2794
87.1218-4.5308-4.26145.30664.89425.3014-0.051-0.11090.39070.53820.26830.3620.842-0.8782-0.03540.3279-0.08220.06880.39350.06970.5408-33.736-18.7557-15.7311
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 60 )
3X-RAY DIFFRACTION3chain 'B' and (resid 402 through 521 )
4X-RAY DIFFRACTION4chain 'B' and (resid 522 through 546 )
5X-RAY DIFFRACTION5chain 'C' and (resid 6 through 20 )
6X-RAY DIFFRACTION6chain 'C' and (resid 21 through 60 )
7X-RAY DIFFRACTION7chain 'D' and (resid 402 through 521 )
8X-RAY DIFFRACTION8chain 'D' and (resid 522 through 546 )

+
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