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- PDB-4i6g: a vertebrate cryptochrome with FAD -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4i6g
Titlea vertebrate cryptochrome with FAD
ComponentsCryptochrome-2
KeywordsTRANSCRIPTION / Cryptochrome / Circadian Clock / Metabolite / Photolyase fold / FAD / Fbxl3 / Periods / Nucleus
Function / homology
Function and homology information


regulation of sodium-dependent phosphate transport / negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / lipid storage / entrainment of circadian clock by photoperiod / photoreceptor activity / response to light stimulus / phosphatase binding / FAD binding ...regulation of sodium-dependent phosphate transport / negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / lipid storage / entrainment of circadian clock by photoperiod / photoreceptor activity / response to light stimulus / phosphatase binding / FAD binding / response to activity / nuclear receptor binding / circadian regulation of gene expression / response to insulin / regulation of circadian rhythm / kinase binding / protein import into nucleus / circadian rhythm / single-stranded DNA binding / glucose homeostasis / damaged DNA binding / transcription cis-regulatory region binding / nuclear speck / negative regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. ...DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Cryptochrome-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsXing, W. / Busino, L. / Hinds, T.R. / Marionni, S.T. / Saifee, N.H. / Bush, M.F. / Pagano, M. / Zheng, N.
CitationJournal: Nature / Year: 2013
Title: SCFFBXL3 ubiquitin ligase targets cryptochromes at their cofactor pocket.
Authors: Xing, W. / Busino, L. / Hinds, T.R. / Marionni, S.T. / Saifee, N.H. / Bush, M.F. / Pagano, M. / Zheng, N.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cryptochrome-2
B: Cryptochrome-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9494
Polymers117,3782
Non-polymers1,5712
Water4,738263
1
A: Cryptochrome-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4752
Polymers58,6891
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cryptochrome-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4752
Polymers58,6891
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.525, 97.525, 128.821
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Cryptochrome-2 /


Mass: 58689.047 Da / Num. of mol.: 2 / Fragment: UNP residues 1-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry2, Kiaa0658 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9R194
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES-imadzole, pH 6.5, 7.2% PEG8000, 20% ethylene glyco(v/v), 0.03M NaF,NaBr,NaI, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 28, 2011
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 60952 / Num. obs: 60952 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 37.22
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.475 / Rsym value: 0.53 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→43.615 Å / SU ML: 0.28 / σ(F): 1.36 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 2003 3.29 %
Rwork0.1973 --
obs0.1987 60952 99.9 %
all-60952 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→43.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7740 0 106 263 8109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098080
X-RAY DIFFRACTIONf_angle_d1.15110983
X-RAY DIFFRACTIONf_dihedral_angle_d15.8692971
X-RAY DIFFRACTIONf_chiral_restr0.0811136
X-RAY DIFFRACTIONf_plane_restr0.0051401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.32441400.25584167X-RAY DIFFRACTION99
2.255-2.3160.32041400.24164195X-RAY DIFFRACTION100
2.316-2.38410.2791400.23044224X-RAY DIFFRACTION100
2.3841-2.46110.27231420.22194220X-RAY DIFFRACTION100
2.4611-2.5490.24251430.20984176X-RAY DIFFRACTION100
2.549-2.65110.28071410.21664212X-RAY DIFFRACTION100
2.6511-2.77170.25151410.21374200X-RAY DIFFRACTION100
2.7717-2.91780.29951400.21214201X-RAY DIFFRACTION100
2.9178-3.10060.28651440.20874211X-RAY DIFFRACTION100
3.1006-3.33990.26191430.20874218X-RAY DIFFRACTION100
3.3399-3.67590.21821470.19024219X-RAY DIFFRACTION100
3.6759-4.20740.2251450.17164226X-RAY DIFFRACTION100
4.2074-5.29940.19821480.17444225X-RAY DIFFRACTION100
5.2994-43.62310.21931490.19924255X-RAY DIFFRACTION99
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)
13.8224-0.09051.4615.03630.59932.5783-0.41170.0218-0.7084-0.45120.12170.4091.1433-0.17760.08630.931-0.13860.29190.3896-0.03920.604325.4751-36.7922.1535
23.27912.88580.065.48310.48532.779-0.37250.2431-0.6272-0.4140.1894-0.25691.04420.24610.18760.76980.02970.2520.3742-0.00050.368735.3584-27.3529-4.6835
31.155-0.94320.09915.47062.18142.1193-0.31410.4905-0.4521-0.58190.00990.58860.5166-0.40620.32020.8034-0.29840.11660.5765-0.12090.674116.4939-28.974-1.3613
44.8342-2.09271.20952.1732-1.33773.2741-0.3708-0.4047-0.52330.49890.02440.53760.4318-0.21820.36830.5329-0.14130.21840.413-0.08440.608714.5393-19.907517.0494
52.63390.39141.37925.83970.26380.7466-0.67730.3409-1.4408-0.26860.0927-1.20461.6340.18960.48241.48310.03610.42090.8814-0.12321.598935.9615-43.9391-3.2208
60.5761-0.2787-0.6241.4148-0.08235.9111-0.0688-0.1099-0.1355-0.1625-0.0838-0.72030.55360.87140.14360.56370.16740.18290.77160.08790.512244.1742-20.2986-2.4221
78.6147-1.1853-3.57947.03612.07066.50360.7042-0.99960.51551.7977-0.0664-0.8485-0.05611.1854-0.19390.76820.0857-0.06210.76890.27970.40738.2507-24.384517.488
80.463-0.3540.00170.2585-0.0152-0.00390.2399-0.15420.26631.1411-0.9093-1.53980.4674-1.32190.35221.4453-0.5583-0.20341.25020.36190.88941.7579-11.850718.3465
95.0647-0.1002-1.50523.63430.66426.2674-0.0522-0.9544-0.02950.4837-0.14030.0640.54570.21050.25650.6174-0.08030.1040.5890.080.426427.024-21.829722.14
103.09980.22640.70844.7920.37031.8196-0.15480.40420.1131-0.4635-0.03310.58910.137-0.48740.24060.3988-0.06650.05540.4282-0.03670.505717.7038-5.62622.9672
114.9885-1.19620.12494.46861.2922.52550.16470.02860.3661-0.0244-0.0429-0.1392-0.38130.3988-0.10570.2717-0.07750.04250.23340.0080.144837.13570.3145.3214
123.31241.2120.29845.3202-0.90121.8127-0.02770.17910.33150.09940.02310.86820.1804-0.3649-0.0590.3011-0.04130.01650.33870.03210.313224.9539-2.78514.2915
134.1692-1.4419-0.25256.288-1.20296.0130.1973-0.56830.47670.5195-0.40030.81110.0975-0.77540.41250.5915-0.17360.12160.5959-0.14920.514230.98556.098116.5462
143.81482.433-0.13075.221-0.59971.82340.2872-0.40690.61590.1566-0.1729-1.3381-0.59660.816-0.09540.4508-0.20690.03840.6145-0.10940.677750.51199.277410.8606
158.18-0.0018-0.14444.33560.81836.40070.0241-0.12331.2658-0.842-0.160.3965-1.2834-1.0867-0.03550.66840.04360.04930.3857-0.0050.638624.922914.08056.5758
161.7264-1.4907-1.06084.45961.0320.7295-0.213-1.5132-1.70880.8144-0.61540.38541.07850.00740.44240.7361-0.21740.22390.74420.04581.019929.3705-11.499912.7036
171.47040.41590.11081.3609-0.59860.1825-0.39460.51870.7224-0.7369-0.4781.2108-0.7647-1.37490.03940.13310.2436-0.21641.3566-0.47921.073415.817317.832732.4926
185.1679-1.64840.76662.35340.78260.8803-0.1817-0.0226-0.6385-0.0503-0.30421.22780.2941-1.16280.19070.3583-0.1126-0.06140.9567-0.26740.743919.78699.930130.9978
190.8146-1.2014-0.04991.9574-0.02550.1911-0.34130.46960.1908-1.1984-0.1830.5922-0.302-0.715-0.27850.73580.4549-0.44591.2003-0.2641.446215.857325.097928.0944
204.1503-0.2635-0.57630.07770.00560.09170.0473-0.04660.15870.04660.07310.5987-0.203-0.3412-0.07940.70960.8522-0.93591.1596-0.30781.768812.896931.721125.6446
212.09650.96040.3253.17280.20470.8570.1960.09610.77710.608-0.15350.299-0.1085-0.3968-0.03070.63810.257-0.08170.8519-0.36261.171527.660833.629147.8605
227.48750.0476-0.50252.6975-2.41882.34610.9710.0403-0.2286-0.04150.46891.0081-0.0222-1.1712-1.15640.675-0.0017-0.08191.5078-0.0821.49675.473710.11333.5487
232.54412.1876-1.28822.58791.12228.6842-0.6170.3287-0.130.2078-0.27510.30630.6194-1.03070.72750.6824-0.30590.10430.7126-0.18290.479229.24811.898726.0976
244.7164-1.0012-2.86183.22511.72872.7614-0.2828-0.6536-0.05891.02390.0260.14340.4654-0.52010.29940.66350.00080.05750.7547-0.07960.502328.500211.148947.8253
251.3576-0.79120.54092.25121.07794.73020.5507-1.2097-0.32611.5267-0.60610.81610.0986-0.4173-0.00211.058-0.05750.17951.4521-0.36120.811628.700221.150562.8378
265.56890.00230.04041.70670.84552.5228-0.22670.36881.1696-0.3756-0.03520.0139-0.8271-0.44960.13630.59950.1391-0.10550.5-0.12840.965741.447231.009335.9091
275.18650.66090.70585.51430.314.04480.1362-0.0209-0.04710.1730.3209-0.65710.29210.2512-0.4110.3080.0642-0.07750.3477-0.13150.317349.667411.664236.9547
283.3498-0.6497-1.85814.47370.08123.7799-0.0971-0.45771.3771-0.36710.24730.0339-0.7332-0.2305-0.09970.33340.0649-0.02510.3145-0.11380.510945.503623.360236.7206
293.57430.5174-0.06370.91341.03193.8609-0.0685-0.6462-0.29390.88210.4368-0.96050.34760.2853-0.36950.69590.2108-0.32640.5149-0.14520.600856.74826.915245.5433
302.4689-3.6338-0.96346.1311-0.39463.53490.3112-0.07270.2972-0.22670.2053-1.33160.09851.2848-0.1030.38960.1946-0.16530.7312-0.33140.844665.15067.913937.0274
315.39520.22061.47138.0684-3.66682.65-1.0441-0.08751.96610.72250.0592-0.8904-1.69620.22110.6761.1954-0.1827-0.14450.9024-0.21321.47958.90737.888738.8507
328.5722-0.73180.80863.7193.22913.04040.1038-1.0601-0.11791.6649-0.01361.15120.4339-0.58210.14721.1210.4964-0.12290.9349-0.16111.060437.574617.944545.6296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 21:52)
2X-RAY DIFFRACTION2(chain A and resid 53:101)
3X-RAY DIFFRACTION3(chain A and resid 102:162)
4X-RAY DIFFRACTION4(chain A and resid 163:189)
5X-RAY DIFFRACTION5(chain A and resid 190:209)
6X-RAY DIFFRACTION6(chain A and resid 210:232)
7X-RAY DIFFRACTION7(chain A and resid 233:243)
8X-RAY DIFFRACTION8(chain A and resid 244:268)
9X-RAY DIFFRACTION9(chain A and resid 269:307)
10X-RAY DIFFRACTION10(chain A and resid 308:341)
11X-RAY DIFFRACTION11(chain A and resid 342:383)
12X-RAY DIFFRACTION12(chain A and resid 384:425)
13X-RAY DIFFRACTION13(chain A and resid 426:440)
14X-RAY DIFFRACTION14(chain A and resid 441:483)
15X-RAY DIFFRACTION15(chain A and resid 484:511)
16X-RAY DIFFRACTION16(chain A and resid 900:900)
17X-RAY DIFFRACTION17(chain B and resid 21:64)
18X-RAY DIFFRACTION18(chain B and resid 65:101)
19X-RAY DIFFRACTION19(chain B and resid 102:127)
20X-RAY DIFFRACTION20(chain B and resid 128:141)
21X-RAY DIFFRACTION21(chain B and resid 142:184)
22X-RAY DIFFRACTION22(chain B and resid 185:208)
23X-RAY DIFFRACTION23(chain B and resid 209:226)
24X-RAY DIFFRACTION24(chain B and resid 227:286)
25X-RAY DIFFRACTION25(chain B and resid 287:308)
26X-RAY DIFFRACTION26(chain B and resid 309:340)
27X-RAY DIFFRACTION27(chain B and resid 341:382)
28X-RAY DIFFRACTION28(chain B and resid 383:425)
29X-RAY DIFFRACTION29(chain B and resid 426:467)
30X-RAY DIFFRACTION30(chain B and resid 468:500)
31X-RAY DIFFRACTION31(chain B and resid 501:511)
32X-RAY DIFFRACTION32(chain B and resid 900:900)

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