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- PDB-4u63: Crystal structure of a bacterial class III photolyase from Agroba... -

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Basic information

Entry
Database: PDB / ID: 4u63
TitleCrystal structure of a bacterial class III photolyase from Agrobacterium tumefaciens at 1.67A resolution
ComponentsDNA photolyase
KeywordsLYASE / PHOTOLYASE / DNA REPAIR / METHENYLTETRAHYDROFOLATE / CYCLOPYRIMIDINE DIMER / FLAVIN / FAD / FLAVOPROTEIN / PHOTOREDUCTION / TRP TRIADE / Double-Stranded / DNA Damage / DNA / Ultraviolet Rays / Agrobacterium tumefaciens
Function / homology
Function and homology information


photoreactive repair / deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / : / FAD binding / DNA binding
Similarity search - Function
DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / 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 ...DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / 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 / Deoxyribodipyrimidine photo-lyase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsScheerer, P. / Zhang, F. / Kalms, J. / von Stetten, D. / Krauss, N. / Oberpichler, I. / Lamparter, T.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Class III Cyclobutane Pyrimidine Dimer Photolyase Structure Reveals a New Antenna Chromophore Binding Site and Alternative Photoreduction Pathways.
Authors: Scheerer, P. / Zhang, F. / Kalms, J. / von Stetten, D. / Krau, N. / Oberpichler, I. / Lamparter, T.
History
DepositionJul 26, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA photolyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,74918
Polymers56,0391
Non-polymers2,71017
Water9,854547
1


  • Idetical with deposited unit
  • defined by software
  • MONOMERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-154 kcal/mol
Surface area22490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.867, 81.867, 195.952
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA photolyase


Mass: 56038.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MRGSHHHHHHGSHVI - Expression Taq / Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / ATCC 33970 / Gene: Atu1218 / Plasmid: PQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: A9CJC9

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Non-polymers , 5 types, 564 molecules

#2: Chemical ChemComp-MHF / 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID


Mass: 457.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N7O6
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 3.51 Å3/Da / Density % sol: 64.96 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 3 M ammonium sulfate, 10% (v/v) glycerol, 75 mM sodium chloride, 12.5 mM tris (hydroxymethyl) amino methane, 1.25 mM ethylenediaminetetraacetic acid.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91842 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2010 / Details: mirrors
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91842 Å / Relative weight: 1
ReflectionResolution: 1.67→34.3 Å / Num. all: 89158 / Num. obs: 89158 / % possible obs: 100 % / Redundancy: 9.2 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.7
Reflection shellResolution: 1.67→1.76 Å / Redundancy: 9 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U3C

1u3c


Resolution: 1.67→34.3 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.115 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18047 4330 4.9 %RANDOM
Rwork0.1562 ---
obs0.15736 84703 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.121 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.43 Å2-0 Å2
2--0.87 Å20 Å2
3----2.82 Å2
Refinement stepCycle: 1 / Resolution: 1.67→34.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 164 547 4510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194231
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9875800
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 297 -
Rwork0.243 6172 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.05330.01750.01870.0937-0.00350.01-0.0015-0.00150.0009-0.0116-0.00130.0073-0.0039-0.00320.00280.01240.0035-0.00090.0059-0.00130.06435.3708-17.0159-37.586
229.377612.253222.78649.698111.803422.52750.9704-1.5761-0.01630.9612-0.81740.181.3274-1.55-0.1530.1412-0.0830.00660.11210.0170.04115.4178-20.3485-36.6257
30.6130.6335-0.16772.832-0.2390.0479-0.0050.0067-0.00510.04880.00570.0247-0.0015-0.002-0.00070.02050.0058-0.00090.0069-0.00150.058337.8533-14.6007-32.0403
40.1571-0.02930.02050.20420.20970.2439-0.0193-0.0776-0.09850.0242-0.00520.07260.0511-0.02450.02450.09520.0333-0.04320.05420.02170.122942.0903-12.1645-41.0314
50.0856-0.0034-0.02120.1643-0.06370.1416-0.0019-0.01850.002-0.01560.00080.0060.0099-0.00910.00110.01970.0068-0.00430.0087-0.0040.073937.6745-17.388-38.6462
64.866-3.04043.64278.73647.955818.04040.11160.1464-0.086-0.1503-0.26820.1968-0.0414-0.15730.15670.090.0043-0.00290.08730.03330.141918.2901-8.99-44.6567
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 478
2X-RAY DIFFRACTION2B1001
3X-RAY DIFFRACTION3C1002
4X-RAY DIFFRACTION4D1001 - 1014
5X-RAY DIFFRACTION5H1 - 547
6X-RAY DIFFRACTION6E1

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