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- PDB-5lfa: Crystal structure of iron-sulfur cluster containing bacterial (6-... -

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Basic information

Entry
Database: PDB / ID: 5lfa
TitleCrystal structure of iron-sulfur cluster containing bacterial (6-4) photolyase PhrB - Y424F mutant with impaired DNA repair activity
Components(6-4) photolyase
KeywordsLYASE / PHOTOLYASE / DNA REPAIR / IRON-SULFUR CLUSTER / FLAVOPROTEIN
Function / homology
Function and homology information


(6-4)DNA photolyase / DNA (6-4) photolyase activity / photoreactive repair / FAD binding / 4 iron, 4 sulfur cluster binding / DNA binding / metal ion binding
Similarity search - Function
Deoxyribodipyrimidine photolyase-related / Photolyase PhrB-like / : / Deoxyribodipyrimidine photo-lyase-related protein / 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, FAD-binding domain-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold ...Deoxyribodipyrimidine photolyase-related / Photolyase PhrB-like / : / Deoxyribodipyrimidine photo-lyase-related protein / 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, FAD-binding domain-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-DLZ / FLAVIN-ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / (6-4) photolyase
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKwiatkowski, D. / Zhang, F. / Krauss, N. / Lamparter, T. / Scheerer, P.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationSFB 740 - B6 Germany
German Research FoundationSFB 1078 - B6 Germany
German Research FoundationCluster of Excellence - Unifying Concepts in Catalysis - D3/E3 Germany
CitationJournal: Photochem. Photobiol. / Year: 2017
Title: Crystal Structures of Bacterial (6-4) Photolyase Mutants with Impaired DNA Repair Activity.
Authors: Zhang, F. / Ma, H. / Bowatte, K. / Kwiatkowski, D. / Mittmann, E. / Qasem, H. / Krau, N. / Zeng, X. / Ren, Z. / Scheerer, P. / Yang, X. / Lamparter, T.
History
DepositionJun 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (6-4) photolyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9487
Polymers59,2081
Non-polymers1,7406
Water2,000111
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-30 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.183, 94.441, 103.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-801-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein (6-4) photolyase / (6-4)DNA photolyase / DNA photolyase PhrB / Photoreactivating enzyme PhrB


Mass: 59207.867 Da / Num. of mol.: 1 / Mutation: Y424F
Source method: isolated from a genetically manipulated source
Details: Y424F mutant
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Gene: phrB, Atu4765 / Plasmid: PET-21B / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: A9CH39, (6-4)DNA photolyase

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Non-polymers , 5 types, 117 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-DLZ / 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol / 6,7-dimethyl-8-(1'-D-ribityl) lumazine


Mass: 326.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18N4O6
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 50.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 MM MES, 5% PEG400, PH 6.0,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.5→69.79 Å / Num. obs: 19657 / % possible obs: 99.51 % / Redundancy: 5.3 % / Biso Wilson estimate: 21 Å2 / CC1/2: 0.963 / Rmerge(I) obs: 0.2 / Net I/σ(I): 5.3
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
PHENIX10.1-2155refinement
XDSBUILT=20160514data reduction
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DJA

4dja


Resolution: 2.5→69.79 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9 / SU B: 24.531 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R Free: 0.288 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23961 1031 5.3 %RANDOM
Rwork0.18071 ---
obs0.18388 18586 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.516 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.34 Å2-0 Å2
3----0.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0 Å0 Å
Luzzati d res low-0 Å
Luzzati sigma a-0 Å
Refinement stepCycle: 1 / Resolution: 2.5→69.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3916 0 102 111 4129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194138
X-RAY DIFFRACTIONr_bond_other_d0.0010.023720
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.9655622
X-RAY DIFFRACTIONr_angle_other_deg0.973.0018497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0395502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.24522.941204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12215618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5511536
X-RAY DIFFRACTIONr_chiral_restr0.0690.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024732
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021035
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_it1.9352.7742002
X-RAY DIFFRACTIONr_mcbond_other1.9282.7732001
X-RAY DIFFRACTIONr_mcangle_it2.7114.1562500
X-RAY DIFFRACTIONr_mcangle_other2.7114.1572501
X-RAY DIFFRACTIONr_scbond_it1.922.8552136
X-RAY DIFFRACTIONr_scbond_other1.9192.8552136
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5324.2243109
X-RAY DIFFRACTIONr_long_range_B_refined3.53850.82917791
X-RAY DIFFRACTIONr_long_range_B_other3.53950.82817791
X-RAY DIFFRACTIONr_rigid_bond_restr2.34637856
X-RAY DIFFRACTIONr_sphericity_free32.756531
X-RAY DIFFRACTIONr_sphericity_bonded13.22257827
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 67 -
Rwork0.242 1365 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -3.943 Å / Origin y: -30.115 Å / Origin z: 11.099 Å
111213212223313233
T0.0041 Å2-0.0025 Å2-0.0012 Å2-0.0034 Å2-0.0002 Å2--0.054 Å2
L0.1085 °2-0.0143 °20.0762 °2-0.0381 °2-0.0495 °2--0.1409 °2
S-0.0015 Å °0.0095 Å °-0.0084 Å °0.0113 Å °-0.0101 Å °0.0063 Å °-0.0186 Å °0.0139 Å °0.0116 Å °

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