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- PDB-9lpg: Crystal structure of maize CRY-GL2 photosignaling complex -

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Basic information

Entry
Database: PDB / ID: 9lpg
TitleCrystal structure of maize CRY-GL2 photosignaling complex
Components
  • Cryptochrome2
  • Protein ECERIFERUM 26-like
KeywordsPLANT PROTEIN / complex
Function / homology
Function and homology information


blue light photoreceptor activity / nucleobase-containing compound metabolic process / acyltransferase activity, transferring groups other than amino-acyl groups / response to stress
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. / Transferase family / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain ...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. / Transferase family / 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 / Chloramphenicol acetyltransferase-like domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Protein ECERIFERUM 26-like / Cryptochrome2
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLiu, Y. / Zhang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of maize CRY-GL2 photosignaling complex
Authors: Liu, Y. / Zhang, P.
History
DepositionJan 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cryptochrome2
E: Protein ECERIFERUM 26-like
B: Cryptochrome2
F: Protein ECERIFERUM 26-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,5256
Polymers246,9544
Non-polymers1,5712
Water59433
1
A: Cryptochrome2
E: Protein ECERIFERUM 26-like
B: Cryptochrome2
F: Protein ECERIFERUM 26-like
hetero molecules

A: Cryptochrome2
E: Protein ECERIFERUM 26-like
B: Cryptochrome2
F: Protein ECERIFERUM 26-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)497,05112
Polymers493,9098
Non-polymers3,1424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Unit cell
Length a, b, c (Å)108.347, 217.056, 228.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cryptochrome2


Mass: 77609.125 Da / Num. of mol.: 2 / Mutation: W368A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 100194126, ZEAMMB73_Zm00001d003477 / Production host: Escherichia coli (E. coli) / References: UniProt: B8A2L5
#2: Protein Protein ECERIFERUM 26-like


Mass: 45868.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A804MAL4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% (w/v) Polyethylene glycol 3,350, 100 mM Bis-tris Propane/Hydrochloric acid pH 6.5, 200 mM Sodium fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 99342 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 0.975 / CC star: 0.994 / Rmerge(I) obs: 0.308 / Rpim(I) all: 0.088 / Rrim(I) all: 0.321 / Χ2: 0.961 / Net I/σ(I): 3.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.8-2.8510.71.42931920.6410.8840.4471.50.91796.4
2.85-2.911.61.27632360.7150.9130.3851.3340.92498.4
2.9-2.9612.31.1532770.7950.9410.3381.20.91799.7
2.96-3.0212.41.00432520.8440.9570.2941.0470.93499.7
3.02-3.0811.90.83332980.8730.9650.250.8710.94899.9
3.08-3.1513.90.84432780.8930.9710.2330.8760.942100
3.15-3.2313.90.70432800.9260.9810.1940.730.942100
3.23-3.3213.80.59132810.930.9820.1640.6140.943100
3.32-3.4213.60.50233070.9510.9870.140.5210.969100
3.42-3.5313.40.42632870.960.990.120.4430.951100
3.53-3.6513.10.37233060.9610.990.1060.3870.954100
3.65-3.8120.30932980.9680.9920.0920.3230.9599.8
3.8-3.9713.80.29433070.9770.9940.0820.3050.979100
3.97-4.1813.70.2733370.9750.9940.0750.280.992100
4.18-4.4413.60.2533050.9760.9940.070.260.971100
4.44-4.7913.30.2433270.9770.9940.0680.250.97899.9
4.79-5.2712.80.23233460.9770.9940.0670.2420.96899.9
5.27-6.0313.80.23533650.9740.9930.0650.2440.978100
6.03-7.5912.60.22433750.970.9920.0650.2340.96599.9
7.59-5012.80.22235270.970.9920.0640.2311.07199.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: 000)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZ3

6lz3


Resolution: 2.8→42.166 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 3263 3.28 %
Rwork0.2317 --
obs0.2329 99342 77.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→42.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13842 0 106 33 13981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714326
X-RAY DIFFRACTIONf_angle_d1.16819524
X-RAY DIFFRACTIONf_dihedral_angle_d23.8795154
X-RAY DIFFRACTIONf_chiral_restr0.1742102
X-RAY DIFFRACTIONf_plane_restr0.0062518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8004-2.84220.3787490.30171372X-RAY DIFFRACTION25
2.8422-2.88660.3285630.28861751X-RAY DIFFRACTION33
2.8866-2.93390.3225620.28972176X-RAY DIFFRACTION40
2.9339-2.98450.3646860.30062565X-RAY DIFFRACTION48
2.9845-3.03880.2871990.28422791X-RAY DIFFRACTION51
3.0388-3.09720.31171020.30813162X-RAY DIFFRACTION58
3.0972-3.16040.29631220.30633473X-RAY DIFFRACTION64
3.1604-3.22910.32941340.29063613X-RAY DIFFRACTION68
3.2291-3.30420.31631310.26783843X-RAY DIFFRACTION71
3.3042-3.38680.33351370.27124129X-RAY DIFFRACTION76
3.3868-3.47830.31251380.26154386X-RAY DIFFRACTION81
3.4783-3.58060.29951620.2564665X-RAY DIFFRACTION87
3.5806-3.69610.26041670.24734916X-RAY DIFFRACTION91
3.6961-3.82810.26181770.23714983X-RAY DIFFRACTION93
3.8281-3.98130.29471820.22365374X-RAY DIFFRACTION100
3.9813-4.16230.2491840.21045388X-RAY DIFFRACTION99
4.1623-4.38160.25051790.20075324X-RAY DIFFRACTION99
4.3816-4.65580.21691840.20555403X-RAY DIFFRACTION100
4.6558-5.01470.24321820.20025359X-RAY DIFFRACTION99
5.0147-5.51840.23081780.21485397X-RAY DIFFRACTION100
5.5184-6.31460.28751840.22315389X-RAY DIFFRACTION100
6.3146-7.9470.24381860.22515348X-RAY DIFFRACTION100
7.947-42.1660.24211750.20645272X-RAY DIFFRACTION97

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