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- PDB-8ijy: Synechococcus elongatus 6-4 photolyase with an 8-HDF as the anten... -

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Basic information

Entry
Database: PDB / ID: 8ijy
TitleSynechococcus elongatus 6-4 photolyase with an 8-HDF as the antenna chromophore and a covalently linked FAD as the catalytic cofactor
ComponentsDeoxyribodipyrimidine photolyase-related protein
KeywordsDNA BINDING PROTEIN / photolyase / 6-4 photoproduct / 8-HDF / covalently linked FAD
Function / homologyPhotolyase PhrB-like / : / Deoxyribodipyrimidine photo-lyase-related protein / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold / FLAVIN-ADENINE DINUCLEOTIDE / Chem-HDF / IRON/SULFUR CLUSTER / Deoxyribodipyrimidine photolyase-related protein
Function and homology information
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsLiu, Y. / Xu, L. / Zhang, P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971199 China
National Natural Science Foundation of China (NSFC)32271287 China
CitationJournal: To Be Published
Title: Synechococcus elongatus 6-4 photolyase with an 8-HDF as the antenna chromophore and a covalently linked FAD as the catalytic cofactor
Authors: Liu, Y. / Xu, L. / Zhang, P.
History
DepositionFeb 28, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyribodipyrimidine photolyase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,13014
Polymers59,6781
Non-polymers2,45213
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-29 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.116, 109.136, 95.217
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Deoxyribodipyrimidine photolyase-related protein


Mass: 59678.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: WP_011377897.1
Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Gene: Synpcc7942_1171 / Plasmid: pETSePhrB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q31P18

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Non-polymers , 6 types, 291 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HDF / 8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE


Mass: 363.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N3O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.23 % / Description: green flat crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% (w/v) PEG 8000 , 100 mM Tris base/ Hydrochloric acid pH 8.5, 200 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: under 100 K liquid nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.38→75.71 Å / Num. obs: 22021 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.051 / Rrim(I) all: 0.157 / Χ2: 0.938 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.4-2.448.50.47210850.9440.9860.1640.5010.97999.9
2.44-2.498.70.4310590.9580.9890.150.4560.96399.7
2.49-2.5390.44711180.9530.9880.1550.4740.96100
2.53-2.5990.41310530.9580.9890.1420.4370.95299.9
2.59-2.6490.36711050.970.9920.1270.3890.978100
2.64-2.78.90.36410830.9720.9930.1270.3860.972100
2.7-2.778.70.31210830.9770.9940.1090.3310.94100
2.77-2.8580.26711000.9760.9940.0950.2840.93799
2.85-2.939.30.2510860.9820.9950.0850.2640.949100
2.93-3.029.50.23110790.9840.9960.0780.2440.969100
3.02-3.139.30.20511050.9880.9970.070.2170.922100
3.13-3.269.30.1710900.9920.9980.0570.1790.936100
3.26-3.419.20.15611030.9910.9980.0530.1650.936100
3.41-3.588.90.12710960.9930.9980.0430.1350.91899.9
3.58-3.818.40.10711190.9950.9990.0370.1140.94399.5
3.81-4.19.60.09910830.9960.9990.0320.1040.93199.7
4.1-4.529.30.09111200.9950.9990.030.0960.879100
4.52-5.178.90.08411190.9960.9990.0280.0890.803100
5.17-6.518.60.0911380.9940.9990.0310.0950.78799.9
6.51-508.30.111970.990.9980.0360.1061.10599.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data scaling
PHASER2.6.1phasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→75.71 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.501 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.685 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18964 1097 5.3 %RANDOM
Rwork0.15082 ---
obs0.15288 19669 93.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.869 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0 Å2-0 Å2
2--0.85 Å2-0 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 2.38→75.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4084 0 149 278 4511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194407
X-RAY DIFFRACTIONr_bond_other_d0.0020.024035
X-RAY DIFFRACTIONr_angle_refined_deg2.4031.9646015
X-RAY DIFFRACTIONr_angle_other_deg1.32339241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12923.75224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37915683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7371530
X-RAY DIFFRACTIONr_chiral_restr0.1290.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214954
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021117
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6643.5562012
X-RAY DIFFRACTIONr_mcbond_other2.6623.5532010
X-RAY DIFFRACTIONr_mcangle_it3.8525.3212512
X-RAY DIFFRACTIONr_mcangle_other3.8525.3222513
X-RAY DIFFRACTIONr_scbond_it3.5443.9152395
X-RAY DIFFRACTIONr_scbond_other3.5443.9152395
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2785.7183492
X-RAY DIFFRACTIONr_long_range_B_refined6.87529.8875426
X-RAY DIFFRACTIONr_long_range_B_other6.80929.715317
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.382→2.444 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 61 -
Rwork0.187 923 -
obs--60.48 %

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