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- PDB-6cny: 2.3 Angstrom Structure of Phosphodiesterase treated Vivid (comple... -

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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


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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: 0 / Refine code: 0

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

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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 / Flavin mononucleotide


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

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Experimental details

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Experiment

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

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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

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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

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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

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