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6wtb

Sort-Tagged Drosophila Cryptochrome

Method: X-RAY DIFFRACTION Dmax: 122.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cryptochrome-1

Drosophila melanogaster

UniProt O77059

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–539 Chain B； UniProt 1–539 Not recorded MG MAGNESIUM ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；4 microliter drop (2 microliter protein solution, 2 microliter well solution) 100 mM Tris (pH 9) 150 mM Magneisum Acetate Tetrahydrate 17% PEG-4000 8 mg/mL sort-tagged WT Drosophila Cryptochrome Resolution 2.58 Å R-free 0.287

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6WTB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4GU5 Structure of Full-length Drosophila Cryptochrome Deposited 2012-08-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–539（539 aa）
Not recorded MG MAGNESIUM ION × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；298 K；50 MM HEPES PH 8.0; 150 MM NACL 5MG/ML PROTEIN MIXED 1:1 WITH 18% PDG 4K, 150 MM MGACETATE, 100 MM TRIS PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Resolution 2.30 Å R-free 0.247
4GU5 Structure of Full-length Drosophila Cryptochrome Deposited 2012-08-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–539（539 aa）
Not recorded MG MAGNESIUM ION × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；298 K；50 MM HEPES PH 8.0; 150 MM NACL 5MG/ML PROTEIN MIXED 1:1 WITH 18% PDG 4K, 150 MM MGACETATE, 100 MM TRIS PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Resolution 2.30 Å R-free 0.247
4JZY Crystal structures of Drosophila Cryptochrome Deposited 2013-04-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–540（540 aa）
Chain B 1–540（540 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NH4 AMMONIUM ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；0.2 M NH4OAc, 20% PEG 3350 , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.34 Å R-free 0.222
4K03 Crystal structure of Drosophila Cryprochrome Deposited 2013-04-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–542（542 aa）
Chain B 1–542（542 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100 mM TrisHCl pH 8.0, 17% PEG 3350, 120 mM Mg-Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.269
7UD0 Room Temperature Drosophila Cryptochrome Deposited 2022-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–539（539 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；pH 8.5；298 K；5 mg/mL twin-strep tagged dCRY (1-539) 100 mM Tris (pH 8.5) 150 mM Magnesium acetate tetrahydrate 18% PEG-4000 Mixed 1:1 in Eppendorf tube; no vortexing
Resolution 3.50 Å R-free 0.294
7UD0 Room Temperature Drosophila Cryptochrome Deposited 2022-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–539（539 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；pH 8.5；298 K；5 mg/mL twin-strep tagged dCRY (1-539) 100 mM Tris (pH 8.5) 150 mM Magnesium acetate tetrahydrate 18% PEG-4000 Mixed 1:1 in Eppendorf tube; no vortexing
Resolution 3.50 Å R-free 0.294
8DD7 The Cryo-EM structure of Drosophila Cryptochrome in complex with Timeless Deposited 2022-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–520（520 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CRY1_DROME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 46–584； UniProt 1–539 Author chain B； PDBConstruct 46–584； UniProt 1–539

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6wtb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6wtb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6wtb
Deposition date deposition_date2020-05-02
Structure title titleSort-Tagged Drosophila Cryptochrome
Keywords keywordsFlavoprotein, Sortylation Linker, CIRCADIAN CLOCK PROTEIN; CIRCADIAN CLOCK PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.65 Å
Radius of gyration Rg (electron density) rg_electron36.39 Å
Forward intensity I(0) i0248740000.00
Molecular weight molecular_weight126400.0 kDa
Excluded volume excluded_volume157600 ų
Envelope volume envelope_volume197610 ų
Hydration-shell volume shell_volume46505 ų
Envelope diameter envelope_diameter132.0 Å
Shell Rg shell_rg41.24 Å
Envelope Rg envelope_rg36.41 Å
Shape Rg shape_rg36.39 Å
Total Rg total_rg36.72 Å
Total atoms total_atoms8907
Residues n_residues1084
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax122.8 Å
Rg (real space) rg_real36.80 Å
Rg uncertainty (real space) rg_real_error1.09 Å
I(0) (real space) i0_real2.4870e+08
I(0) uncertainty (real space) i0_real_error4.0660e+06
Rg (reciprocal space) rg_reciprocal36.71 Å
I(0) (reciprocal space) i0_reciprocal248700000.0000
Solution quality estimate total_estimate0.6751
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary120.0 Å
Skewness Skewness skewness0.416
Kurtosis Kurtosis kurtosis-0.435
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha100200000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 0.159; Positv: 1.000; Valcen: 0.885; Smooth: 0.852
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)