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- PDB-1u3c: Crystal Structure of the PHR domain of Cryptochrome 1 from Arabid... -

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Basic information

Entry
Database: PDB / ID: 1u3c
TitleCrystal Structure of the PHR domain of Cryptochrome 1 from Arabidopsis thaliana
ComponentsCryptochrome 1 apoprotein
KeywordsSIGNALING PROTEIN / photolyase / AMPPNP
Function / homology
Function and homology information


detection of light stimulus / photoprotection / singlet oxygen-mediated programmed cell death / negative regulation of lateral root development / positive regulation of shade avoidance / positive regulation of systemic acquired resistance / regulation of secondary cell wall biogenesis / plant organ development / regulation of unidimensional cell growth / response to red light ...detection of light stimulus / photoprotection / singlet oxygen-mediated programmed cell death / negative regulation of lateral root development / positive regulation of shade avoidance / positive regulation of systemic acquired resistance / regulation of secondary cell wall biogenesis / plant organ development / regulation of unidimensional cell growth / response to red light / auxin transport / flavin adenine dinucleotide metabolic process / response to absence of light / anthocyanin-containing compound metabolic process / response to strigolactone / regulation of meristem growth / regulation of leaf morphogenesis / circadian regulation of calcium ion oscillation / response to low fluence blue light stimulus by blue low-fluence system / positive regulation of anion channel activity / blue light signaling pathway / response to far red light / response to high light intensity / response to magnetism / phototropism / stomatal movement / photomorphogenesis / response to blue light / positive regulation of defense response to bacterium / regulation of hydrogen peroxide metabolic process / blue light photoreceptor activity / response to water deprivation / regulation of reactive oxygen species metabolic process / response to temperature stimulus / response to light stimulus / FAD binding / regulation of circadian rhythm / PML body / defense response / circadian rhythm / kinase activity / regulation of gene expression / protein autophosphorylation / nuclear body / protein kinase activity / apoptotic process / protein homodimerization activity / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Cryptochrome C-terminal / Blue/Ultraviolet sensing protein C terminal / Cryptochrome, plant / DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / 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 C-terminal / Blue/Ultraviolet sensing protein C terminal / Cryptochrome, plant / DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / 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 / HEXANE-1,6-DIOL / ETHYL DIMETHYL AMMONIO PROPANE SULFONATE / Cryptochrome-1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBrautigam, C.A. / Smith, B.S. / Ma, Z. / Palnitkar, M. / Tomchick, D.R. / Machius, M. / Deisenhofer, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana.
Authors: Brautigam, C.A. / Smith, B.S. / Ma, Z. / Palnitkar, M. / Tomchick, D.R. / Machius, M. / Deisenhofer, J.
History
DepositionJul 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Cryptochrome 1 apoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8078
Polymers57,6001
Non-polymers1,2077
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.430, 169.430, 104.245
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cryptochrome 1 apoprotein / Blue light photoreceptor


Mass: 57599.879 Da / Num. of mol.: 1 / Fragment: PHR domain, residues 1-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CRY1 / Plasmid: PMAL-C2-ATCRY / Production host: Escherichia coli (E. coli) / References: UniProt: Q43125

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Non-polymers , 6 types, 75 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-NDS / ETHYL DIMETHYL AMMONIO PROPANE SULFONATE


Mass: 195.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3S
#6: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.7 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 309 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: glycerol, MES, sulfobetaine-195, 1,6-hexanediol, sodium, potassium tartrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 309K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 21, 2004
RadiationMonochromator: Double-crystal monochromator, Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 26452 / Num. obs: 26452 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 26.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2627 / % possible all: 97.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: E.coli DNA photolyase, pdb entry 1DNP

1dnp


Resolution: 2.6→34.6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 200699.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: If no electron density was observed for the side chain of a residue, the occupancy for the side-chain atoms was set to 0.00.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2477 9.9 %RANDOM
Rwork0.205 ---
all0.21 25083 --
obs0.205 25083 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.9863 Å2 / ksol: 0.333542 e/Å3
Displacement parametersBiso mean: 47.9 Å2
Baniso -1Baniso -2Baniso -3
1-8.79 Å211.91 Å20 Å2
2--8.79 Å20 Å2
3----17.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3941 0 85 68 4094
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it3.411.5
X-RAY DIFFRACTIONc_mcangle_it4.912
X-RAY DIFFRACTIONc_scbond_it5.822
X-RAY DIFFRACTIONc_scangle_it7.672.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 395 10.6 %
Rwork0.339 3340 -
obs--82.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4FAD_RIBITOL_DRG.PARAMFAD_RIBITOL_DRG.TOP
X-RAY DIFFRACTION5SB195_DRG.PARAMSB195_DRG.TOP

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