[English] 日本語
Yorodumi
- PDB-6cny: 2.3 Angstrom Structure of Phosphodiesterase treated Vivid (comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cny
Title2.3 Angstrom Structure of Phosphodiesterase treated Vivid (complex with FMN)
ComponentsVivid PAS protein VVD
KeywordsCIRCADIAN CLOCK PROTEIN / LOV Domain / flavin / photoreceptor / circadian clock
Function / homology
Function and homology information


nucleotide binding / nucleus
Similarity search - Function
PAS domain / PAS domain / Beta-Lactamase / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Vivid PAS protein VVD
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZoltowski, B.D. / Shabalin, I.G. / Kowiel, M. / Porebski, P.J. / Crane, B.R. / Bilwes, A.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Searle Scholars Program United States
Citation
Journal: Science / Year: 2007
Title: Conformational switching in the fungal light sensor Vivid.
Authors: Zoltowski, B.D. / Schwerdtfeger, C. / Widom, J. / Loros, J.J. / Bilwes, A.M. / Dunlap, J.C. / Crane, B.R.
#1: Journal: Bioinformatics / Year: 2018
Title: Automatic Recognition of Ligands in Electron Density by Machine Learning.
Authors: Kowiel, M. / Brzezinski, D. / Porebski, P.J. / Shabalin, I.G. / Jaskolski, M. / Minor, W.
History
DepositionMar 9, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionMar 21, 2018ID: 2PDT
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity / Item: _entity.formula_weight
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Structure summary
Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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: Vivid PAS protein VVD
B: Vivid PAS protein VVD
C: Vivid PAS protein VVD
D: Vivid PAS protein VVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8128
Polymers68,9874
Non-polymers1,8254
Water8,593477
1
A: Vivid PAS protein VVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7032
Polymers17,2471
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vivid PAS protein VVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7032
Polymers17,2471
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Vivid PAS protein VVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7032
Polymers17,2471
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Vivid PAS protein VVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7032
Polymers17,2471
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.120, 80.570, 64.110
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

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
11GLYGLYCYSCYSAA43 - 1838 - 148
21GLYGLYCYSCYSBB43 - 1838 - 148
12THRTHRGLUGLUAA38 - 1843 - 149
22THRTHRGLUGLUCC38 - 1843 - 149
13GLYGLYCYSCYSAA43 - 1838 - 148
23GLYGLYCYSCYSDD43 - 1838 - 148
14GLYGLYCYSCYSBB43 - 1838 - 148
24GLYGLYCYSCYSCC43 - 1838 - 148
15GLYGLYGLUGLUBB43 - 1848 - 149
25GLYGLYGLUGLUDD43 - 1848 - 149
16GLYGLYCYSCYSCC43 - 1838 - 148
26GLYGLYCYSCYSDD43 - 1838 - 148

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Vivid PAS protein VVD


Mass: 17246.729 Da / Num. of mol.: 4 / Fragment: residues 37-184
Source method: isolated from a genetically manipulated source
Details: VVD (UniProtKB - Q9C3Y6) was N-terminally truncated by 36 residues
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: vvd, G17A4.050, GE21DRAFT_9175 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q9C3Y6
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O
Compound detailsthe protein was treated with phosphodiesterase, which resulted in hydrolysis of FAD into FMN
Nonpolymer detailsFMN was created by phosphodiesterase treatment of bound FAD

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: An equal volume (2 uL) of protein dissolved in a buffer containing 50 mM HEPES pH 8.0, 150 mM NaCl and 13% glycerol was mixed with the reservoir solution containing 100 mM trisodium citrate ...Details: An equal volume (2 uL) of protein dissolved in a buffer containing 50 mM HEPES pH 8.0, 150 mM NaCl and 13% glycerol was mixed with the reservoir solution containing 100 mM trisodium citrate pH 5.6, 100 mM ammonium acetate and 30% PEG 5K MME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2005
RadiationMonochromator: Double silicon crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 38172 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 25.4
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.87 / Num. unique obs: 2529 / % possible all: 89.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G28

1g28


Resolution: 2.1→45.34 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.674 / SU ML: 0.105 / SU R Cruickshank DPI: 0.0423 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.035
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 1054 2.8 %RANDOM
Rwork0.1629 ---
obs0.164 36724 99.05 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 135.46 Å2 / Biso mean: 45.699 Å2 / Biso min: 14.24 Å2
Baniso -1Baniso -2Baniso -3
1-17.3 Å20 Å21.62 Å2
2---23.23 Å2-0 Å2
3---5.93 Å2
Refinement stepCycle: final / Resolution: 2.1→45.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4587 0 93 477 5157
Biso mean--30.44 45.47 -
Num. residues----579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194816
X-RAY DIFFRACTIONr_bond_other_d0.0020.024378
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9666527
X-RAY DIFFRACTIONr_angle_other_deg0.999310182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.075574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86224.336226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95315830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2351535
X-RAY DIFFRACTIONr_chiral_restr0.0990.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215663
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02952
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A89900.06
12B89900.06
21A94820.04
22C94820.04
31A89860.06
32D89860.06
41B90000.06
42C90000.06
51B91740.04
52D91740.04
61C89940.07
62D89940.07
LS refinement shellResolution: 2.101→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 41 -
Rwork0.26 2488 -
all-2529 -
obs--90.71 %
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)
13.1046-1.48012.71995.0918-3.467711.5094-0.07420.09160.2745-0.0662-0.1798-0.2081-0.06170.25710.2540.04060.02040.05240.0746-0.00220.1505-7.48853.9134.903
26.0527-0.2236-1.14864.57660.63974.8371-0.10990.35010.1163-0.29450.04180.1953-0.1125-0.32690.0680.10440.00110.05240.08990.01240.1635-4.74147.6851.623
34.23292.32712.7776.43481.66745.841-0.1319-0.2258-0.2030.35670.01980.44310.3586-0.25590.11210.09530.01930.09190.10750.01880.1136-8.56937.4688.054
42.8812-0.2563-0.92025.19233.90263.7461-0.1133-0.2656-0.32660.50270.1353-0.40110.43470.3104-0.02190.12870.07320.03470.21470.08460.28765.42334.398-1.53
51.65920.3446-0.39566.83171.14821.9521-0.00560.08940.0231-0.276-0.04750.0045-0.0952-0.08750.05310.04430.01190.02710.10370.01660.0726-2.40144.236-1.834
66.2209-1.78980.80114.86040.67342.0864-0.03820.16890.20350.10980.0825-0.0455-0.0564-0.0076-0.04440.10280.0213-0.00520.1790.01950.2007-24.88265.363.99
73.1812-3.069-0.971112.2514-9.941113.5349-0.3059-0.28920.61831.3414-0.0156-0.7626-0.7910.37230.32150.4395-0.02440.03210.2908-0.06110.5101-33.68477.6343.945
824.042712.5994-9.51219.6409-9.89595.6244-1.79512.03810.64020.60822.22850.62580.1074-1.2321-0.43340.5875-0.1334-0.08020.6738-0.22040.8895-38.99481.6234.992
95.0186-4.37791.221611.1642-0.6090.32850.29390.31080.00360.0852-0.37631.02740.08640.09360.08230.1830.06920.02580.45350.04160.3425-39.44375.166-5.668
102.6359-1.46850.29847.21280.08051.69870.17380.36580.3504-0.1036-0.2731-0.2158-0.08450.02650.09920.09590.02970.00490.27150.03310.2939-28.87968.377-1.406
112.6382-1.5068-2.00334.48562.61146.3054-0.1170.1806-0.2695-0.0923-0.08750.13580.2633-0.11690.20450.0333-0.01240.02780.07290.00360.13537.0726.70235.729
124.40610.64110.01444.4532-0.65654.1732-0.14860.1532-0.0992-0.07860.0377-0.4259-0.04730.31430.11080.050.00990.00530.0548-0.00340.11217.22337.37536.34
132.0965-0.86043.05492.907-3.02886.8777-0.1458-0.23310.22530.27790.15040.2146-0.4137-0.3746-0.00470.14450.03480.02920.1032-0.02950.1687-2.70447.64734.744
141.6463-1.59530.017810.0978-2.59324.15880.12060.1648-0.1945-0.22030.1330.64190.1945-0.1682-0.25360.102-0.0163-0.02020.1071-0.00930.1489-4.80835.74525.188
151.5003-0.60420.54228.536-1.24022.74480.00540.11450.0892-0.3557-0.0546-0.15380.00390.22730.04920.03150.00660.01820.1278-0.00860.10494.15237.41631.542
166.3677-2.45230.00634.8553-1.04263.163-0.01080.40020.1229-0.0306-0.0185-0.20380.01640.07130.02940.08130.0130.06730.1207-0.00010.181524.54720.12232.986
179.55782.33630.34875.59160.12430.8304-0.0416-0.3794-0.71220.40930.0170.20060.08350.07620.02470.13920.0380.08460.16590.02150.245225.0796.9540.58
184.97690.02150.22513.30787.67667.9056-0.2257-0.1007-1.16190.94520.1071-0.17430.66590.1970.11850.12340.07330.06190.17580.05320.371733.0343.11337.718
196.1645-2.78980.59527.8704-1.18170.18410.236-0.067-0.33780.2277-0.3079-0.4864-0.01840.03810.07180.28730.15710.00120.4393-0.10840.51139.7371.71428.868
203.1442-1.13710.18877.9149-0.38092.16380.18780.4496-0.1883-0.0967-0.2209-0.12460.07070.17780.03320.06290.03370.03370.2421-0.01830.190429.85412.2730.281
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 60
2X-RAY DIFFRACTION2A61 - 84
3X-RAY DIFFRACTION3A85 - 105
4X-RAY DIFFRACTION4A106 - 136
5X-RAY DIFFRACTION5A137 - 184
6X-RAY DIFFRACTION6B43 - 105
7X-RAY DIFFRACTION7B106 - 114
8X-RAY DIFFRACTION8B115 - 120
9X-RAY DIFFRACTION9B121 - 139
10X-RAY DIFFRACTION10B140 - 184
11X-RAY DIFFRACTION11C38 - 62
12X-RAY DIFFRACTION12C63 - 98
13X-RAY DIFFRACTION13C99 - 128
14X-RAY DIFFRACTION14C129 - 148
15X-RAY DIFFRACTION15C149 - 184
16X-RAY DIFFRACTION16D43 - 81
17X-RAY DIFFRACTION17D82 - 102
18X-RAY DIFFRACTION18D103 - 115
19X-RAY DIFFRACTION19D116 - 134
20X-RAY DIFFRACTION20D135 - 184

+
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