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- PDB-2j4d: Cryptochrome 3 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 2j4d
TitleCryptochrome 3 from Arabidopsis thaliana
ComponentsCRYPTOCHROME DASH
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / CRYPTOCHROME / FLAVOPROTEIN / FAD / MITOCHONDRION / PLASTID / CHROMOPHORE / CHLOROPLAST / TRANSIT PEPTIDE / BLUE-LIGHT RESPONSE
Function / homology
Function and homology information


photoreactive repair / deoxyribodipyrimidine photo-lyase activity / photoreceptor activity / FAD binding / chloroplast / mitochondrion / DNA binding / ATP binding
Similarity search - Function
Cryptochrome DASH / 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 ...Cryptochrome DASH / 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 / 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID / Cryptochrome DASH, chloroplastic/mitochondrial
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKlar, T. / Pokorny, R. / Batschauer, A. / Essen, L.-O.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Cryptochrome 3 from Arabidopsis Thaliana: Structural and Functional Analysis of its Complex with a Folate Light Antenna
Authors: Klar, T. / Pokorny, R. / Moldt, J. / Batschauer, A. / Essen, L.-O.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization and Preliminary X-Ray Analysis of Cryptochrome 3 from Arabidopsis Thaliana
Authors: Pokorny, R. / Klar, T. / Essen, L.-O. / Batschauer, A.
History
DepositionAug 28, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRYPTOCHROME DASH
B: CRYPTOCHROME DASH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,1516
Polymers120,6652
Non-polymers2,4864
Water13,457747
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A: CRYPTOCHROME DASH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5763
Polymers60,3331
Non-polymers1,2432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CRYPTOCHROME DASH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5763
Polymers60,3331
Non-polymers1,2432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.298, 116.782, 135.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.88463, 0.39435, 0.24881), (0.40088, 0.37066, 0.8378), (0.23816, 0.84089, -0.48599)
Vector: 35.1292, 41.44744, -84.5062)

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Components

#1: Protein CRYPTOCHROME DASH / CRYPTOCHROME 3


Mass: 60332.621 Da / Num. of mol.: 2
Fragment: MATURE PROTEIN WITHOUT PLASTID IMPORT SEQUENCE, RESIDUES 45-569
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PQE-60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15-PREP4 / References: UniProt: Q84KJ5
#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: Chemical ChemComp-MHF / 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID


Mass: 457.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N7O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 747 / 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: 2.48 Å3/Da / Density % sol: 44 %
Crystal growpH: 4.6
Details: 10 MG/ML PROTEIN, 85 MM NA-CITRATE PH 4.6, 170 MM NH4-ACETATE, 21.5 W/V-% PEG 4000 AND 7.5 V/V-% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8125
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8125 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 93259 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4.47 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.4
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / % possible all: 85.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NP7

1np7


Resolution: 1.9→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 1420 1.5 %SHELL-WISE
Rwork0.1886 ---
obs0.1886 93157 97.6 %-
Solvent computationSolvent model: BULK / Bsol: 48.4007 Å2 / ksol: 0.357165 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.036 Å20 Å2
3----0.007 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8119 0 172 747 9038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.574
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 28
RfactorNum. reflection% reflection
Rfree0.39 71 1.5 %
Rwork0.319 4692 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4COFACS.PARAMCOFACS.TOP

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