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- PDB-3gdi: Mammalian Clock Protein mPER2 - Crystal Structure of a PAS Domain... -

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Basic information

Entry
Database: PDB / ID: 3gdi
TitleMammalian Clock Protein mPER2 - Crystal Structure of a PAS Domain Fragment
ComponentsPeriod circadian protein homolog 2
KeywordsTRANSCRIPTION / tandem PAS domains / Biological rhythms / Nucleus / Phosphoprotein / Transcription regulation
Function / homology
Function and homology information


regulation of glutamate uptake involved in transmission of nerve impulse / circadian regulation of translation / negative regulation of termination of DNA-templated transcription / negative regulation of fat cell proliferation / negative regulation of transcription regulatory region DNA binding / negative regulation of circadian rhythm / lactate biosynthetic process / histone methyltransferase binding / pre-mRNA binding / glycogen biosynthetic process ...regulation of glutamate uptake involved in transmission of nerve impulse / circadian regulation of translation / negative regulation of termination of DNA-templated transcription / negative regulation of fat cell proliferation / negative regulation of transcription regulatory region DNA binding / negative regulation of circadian rhythm / lactate biosynthetic process / histone methyltransferase binding / pre-mRNA binding / glycogen biosynthetic process / RNA polymerase binding / entrainment of circadian clock by photoperiod / regulation of insulin secretion / white fat cell differentiation / regulation of neurogenesis / regulation of vasoconstriction / negative regulation of protein ubiquitination / transcription corepressor binding / fatty acid metabolic process / response to ischemia / gluconeogenesis / nuclear receptor binding / circadian regulation of gene expression / regulation of circadian rhythm / kinase binding / histone deacetylase binding / circadian rhythm / positive regulation of cold-induced thermogenesis / DNA-binding transcription factor binding / transcription coactivator activity / transcription cis-regulatory region binding / regulation of cell cycle / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Period circadian protein homolog 3-like, PAS-A domain / 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. ...: / Period circadian protein homolog 3-like, PAS-A domain / 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 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsHennig, S. / Wolf, E.
CitationJournal: Plos Biol. / Year: 2009
Title: Structural and functional analyses of PAS domain interactions of the clock proteins Drosophila PERIOD and mouse PERIOD2.
Authors: Hennig, S. / Strauss, H.M. / Vanselow, K. / Yildiz, O. / Schulze, S. / Arens, J. / Kramer, A. / Wolf, E.
History
DepositionFeb 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2016Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 2023Group: 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 / 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

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Assembly

Deposited unit
A: Period circadian protein homolog 2
B: Period circadian protein homolog 2


Theoretical massNumber of molelcules
Total (without water)70,1822
Polymers70,1822
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-22 kcal/mol
Surface area25670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.670, 63.380, 72.510
Angle α, β, γ (deg.)90.000, 102.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Period circadian protein homolog 2 / Circadian clock protein PERIOD 2 / mPER2


Mass: 35091.195 Da / Num. of mol.: 2 / Fragment: UNP residues 170-473
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Per2 / Plasmid: pGEX6P2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: O54943
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 23% PEG8000, 100 mM HEPES pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97805 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97805 Å / Relative weight: 1
ReflectionResolution: 2.4→19.92 Å / Num. obs: 23980 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.77 % / Biso Wilson estimate: 23.9 Å2 / Limit h max: 28 / Limit h min: -29 / Limit k max: 26 / Limit k min: -29 / Limit l max: 30 / Limit l min: 0 / Observed criterion F max: 1438193.13 / Observed criterion F min: 9.078 / Rmerge(I) obs: 0.067 / Rsym value: 0.074 / Net I/σ(I): 17.15
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 3 / Num. measured obs: 16191 / Num. unique all: 2742 / Num. unique obs: 2742 / Rsym value: 0.667 / % possible all: 98

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å19.92 Å
Translation3 Å19.92 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
CNS1.2refinement
PDB_EXTRACT3.006data extraction
MAR345data collection
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WA9

1wa9


Resolution: 2.4→19.92 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1199 2.9 %RANDOM
Rwork0.224 ---
all0.264 24316 --
obs0.264 23980 57.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 57.154 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 190.97 Å2 / Biso mean: 57 Å2 / Biso min: 29.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.119 Å20 Å2-18.522 Å2
2---17.143 Å20 Å2
3---17.024 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.54 Å
Luzzati d res high-2.4
Refinement stepCycle: LAST / Resolution: 2.4→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4102 0 0 198 4300
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d1.03
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection Rfree: 5 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.4-2.510.391470.39327980.0323009294597.9
2.51-2.640.3791470.32728060.0313021295397.7
2.64-2.810.3731500.28928440.033027299498.9
2.81-3.020.3121500.27328400.0253044299098.2
3.02-3.320.2621500.22728580.0213038300899
3.32-3.80.2611490.20628350.0213017298498.9
3.8-4.780.231520.18628870.0193066303999.1
4.78-19.920.2751540.21229130.0223113306798.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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