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- PDB-4dj2: Unwinding the Differences of the Mammalian PERIOD Clock Proteins ... -

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Basic information

Entry
Database: PDB / ID: 4dj2
TitleUnwinding the Differences of the Mammalian PERIOD Clock Proteins from Crystal Structure to Cellular Function
ComponentsPeriod circadian protein homolog 1
KeywordsPROTEIN BINDING / PAS domains / circadian clock protein
Function / homology
Function and homology information


: / circadian regulation of translation / regulation of hair cycle / : / : / negative regulation of glucocorticoid receptor signaling pathway / regulation of p38MAPK cascade / negative regulation of JNK cascade / post-transcriptional regulation of gene expression / E-box binding ...: / circadian regulation of translation / regulation of hair cycle / : / : / negative regulation of glucocorticoid receptor signaling pathway / regulation of p38MAPK cascade / negative regulation of JNK cascade / post-transcriptional regulation of gene expression / E-box binding / regulation of cytokine production involved in inflammatory response / entrainment of circadian clock by photoperiod / transcription factor binding / response to light stimulus / regulation of sodium ion transport / negative regulation of canonical NF-kappaB signal transduction / response to cAMP / transcription corepressor binding / circadian regulation of gene expression / regulation of circadian rhythm / chromatin DNA binding / kinase binding / circadian rhythm / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Period circadian-like, C-terminal / Period protein 2/3C-terminal region / PAS fold-3 / PAS fold / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily ...Period circadian-like, C-terminal / Period protein 2/3C-terminal region / PAS fold-3 / PAS fold / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Period circadian protein homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKucera, N. / Schmalen, I. / Hennig, S. / Oellinger, R. / Strauss, H.M. / Grudziecki, A. / Wieczorek, C. / Kramer, A. / Wolf, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Unwinding the differences of the mammalian PERIOD clock proteins from crystal structure to cellular function.
Authors: Kucera, N. / Schmalen, I. / Hennig, S. / Ollinger, R. / Strauss, H.M. / Grudziecki, A. / Wieczorek, C. / Kramer, A. / Wolf, E.
History
DepositionFeb 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Period circadian protein homolog 1
B: Period circadian protein homolog 1
C: Period circadian protein homolog 1
D: Period circadian protein homolog 1


Theoretical massNumber of molelcules
Total (without water)143,0074
Polymers143,0074
Non-polymers00
Water1,38777
1
A: Period circadian protein homolog 1
C: Period circadian protein homolog 1


Theoretical massNumber of molelcules
Total (without water)71,5042
Polymers71,5042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-15 kcal/mol
Surface area25100 Å2
MethodPISA
2
B: Period circadian protein homolog 1
D: Period circadian protein homolog 1


Theoretical massNumber of molelcules
Total (without water)71,5042
Polymers71,5042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-15 kcal/mol
Surface area24400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.340, 56.870, 100.950
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Period circadian protein homolog 1 / mPER1 / Circadian clock protein PERIOD 1 / Circadian pacemaker protein Rigui


Mass: 35751.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Per1, Per, Rigui / Production host: Escherichia coli (E. coli) / References: UniProt: O35973
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.01 Å3/Da / Density % sol: 38.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Tris, 0.15 M NH4OAc, 16% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9807 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2010
RadiationMonochromator: Silicium 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9807 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 30071 / Num. obs: 29780 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.75→2.8 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
go.comdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→49.549 Å / SU ML: 0.48 / σ(F): 2.01 / Phase error: 31.19 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2823 1996 6.71 %RANDOM
Rwork0.2085 ---
all0.2254 30071 --
obs0.2138 29744 98.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.33 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.8954 Å20 Å2-0.4322 Å2
2---1.9024 Å2-0 Å2
3---9.7978 Å2
Refinement stepCycle: LAST / Resolution: 2.75→49.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8093 0 0 77 8170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098306
X-RAY DIFFRACTIONf_angle_d1.29111338
X-RAY DIFFRACTIONf_dihedral_angle_d16.4152933
X-RAY DIFFRACTIONf_chiral_restr0.0791300
X-RAY DIFFRACTIONf_plane_restr0.0071467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.81880.42051440.30611989X-RAY DIFFRACTION100
2.8188-2.8950.32881380.28191994X-RAY DIFFRACTION100
2.895-2.98020.35751430.24281953X-RAY DIFFRACTION100
2.9802-3.07630.33211430.24851956X-RAY DIFFRACTION100
3.0763-3.18630.35591380.23112000X-RAY DIFFRACTION100
3.1863-3.31380.35321450.23282005X-RAY DIFFRACTION99
3.3138-3.46460.30771330.20911953X-RAY DIFFRACTION99
3.4646-3.64720.30531420.20131973X-RAY DIFFRACTION99
3.6472-3.87560.28011450.18832009X-RAY DIFFRACTION99
3.8756-4.17470.22571400.16911942X-RAY DIFFRACTION99
4.1747-4.59460.2661500.15641999X-RAY DIFFRACTION99
4.5946-5.25880.27481450.17611992X-RAY DIFFRACTION98
5.2588-6.6230.241440.20591966X-RAY DIFFRACTION98
6.623-49.55650.22931460.21922017X-RAY DIFFRACTION96
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)
10.9548-0.7883-0.53323.38990.43611.8737-0.13080.1954-0.21710.0584-0.03650.58510.45570.23250.00040.2885-0.0062-0.01180.3542-0.07990.506475.3818-13.708628.9073
23.00370.0970.91051.1574-0.10082.0553-0.0740.10190.36320.0456-0.09350.0987-0.2822-0.21540.00010.30440.0429-0.00150.2724-0.08220.291160.18313.611638.538
31.35092.10320.53024.08590.86032.3348-0.2181-0.12520.2617-0.10250.22050.63410.0931-0.0030.00040.24320.01020.01390.2957-0.08980.426125.227513.710421.17
42.85-0.2882-1.59771.2818-0.35821.8337-0.13540.1674-0.5833-0.1117-0.0237-0.22180.2345-0.1226-0.00010.2531-0.0482-0.01310.2767-0.0940.219310.0758-13.938211.9389
52.92081.09050.26252.92191.56831.60190.9661-0.517-0.68470.3213-0.4924-1.1480.1311-0.02680.19060.4317-0.2758-0.30610.50860.3510.505547.1832-13.198622.3411
62.19431.59530.57523.04360.55880.3374-0.34330.5077-0.2685-0.70070.4030.32030.2972-0.0671-0.00150.3183-0.1476-0.02950.28850.04560.138662.628611.13879.839
71.3251-1.5224-0.32434.0990.22081.00520.75790.51810.3966-0.3287-0.4931-1.354-0.4585-0.0960.07180.43030.29680.24230.64260.23590.4125-2.754312.036328.2397
82.2244-1.7282-0.09633.08770.41370.1067-0.359-0.54370.11440.76410.45460.3781-0.0506-0.23620.00520.36650.14930.04640.2630.04570.156512.433-11.540140.4643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 210:342 )
2X-RAY DIFFRACTION2(CHAIN A AND RESSEQ 358:502 )
3X-RAY DIFFRACTION3(CHAIN B AND RESSEQ 210:342 )
4X-RAY DIFFRACTION4(CHAIN B AND RESSEQ 358:502 )
5X-RAY DIFFRACTION5(CHAIN C AND RESSEQ 210:342 )
6X-RAY DIFFRACTION6(CHAIN C AND RESSEQ 358:502 )
7X-RAY DIFFRACTION7(CHAIN D AND RESSEQ 212:342 )
8X-RAY DIFFRACTION8(CHAIN D AND RESSEQ 358:502 )

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