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- PDB-2r9a: Crystal structure of human XLF -

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Basic information

Entry
Database: PDB / ID: 2r9a
TitleCrystal structure of human XLF
ComponentsNon-homologous end-joining factor 1
KeywordsPROTEIN BINDING / XLF / Cernunnos / non-homologous end joining / DNA Double Strand Break Repair / Alternative splicing / Disease mutation / DNA damage / DNA repair / Nucleus
Function / homology
Function and homology information


positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA end binding / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / response to ionizing radiation / T cell differentiation / DNA polymerase binding ...positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA end binding / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / response to ionizing radiation / T cell differentiation / DNA polymerase binding / B cell differentiation / central nervous system development / Nonhomologous End-Joining (NHEJ) / fibrillar center / double-strand break repair via nonhomologous end joining / site of double-strand break / nucleoplasm / nucleus
Similarity search - Function
Helix hairpin bin / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / XLF, N-terminal / XLF N-terminal domain / XRCC4-like, N-terminal domain superfamily / Beta Complex / Helix Hairpins / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Non-homologous end-joining factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsAndres, S.N. / Junop, M.S.
CitationJournal: Mol.Cell
Title: Crystal Structure of Human XLF: A Twist in Nonhomologous DNA End-Joining
Authors: Andres, S.N. / Modesit, M. / Tsai, C.J. / Chu, G. / Junop, M.S.
History
DepositionSep 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-homologous end-joining factor 1
B: Non-homologous end-joining factor 1


Theoretical massNumber of molelcules
Total (without water)53,4172
Polymers53,4172
Non-polymers00
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.460, 86.950, 91.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe dimer present within the asymmetric unit is believed to represent the biological assembly. This protein elutes from a gel filtration column with an apparent molecular mass equivalent to a dimer of XLF.

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Components

#1: Protein Non-homologous end-joining factor 1 / Protein cernunnos / XRCC4-like factor


Mass: 26708.400 Da / Num. of mol.: 2 / Fragment: N-terminal fragment, unp residues 1-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NHEJ1, XLF / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta(DE3) / References: UniProt: Q9H9Q4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8
Details: pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 18163 / Num. obs: 18163 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.7 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 11.4
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.859 / SU B: 18.735 / SU ML: 0.223 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28674 1031 6.8 %RANDOM
Rwork0.25083 ---
all0.2952 18163 --
obs0.25329 14110 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.424 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å20 Å2
2--2.24 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 0 282 3744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223537
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.9694795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3155429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.12324.847163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.21315635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6091517
X-RAY DIFFRACTIONr_chiral_restr0.1120.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022635
X-RAY DIFFRACTIONr_nbd_refined0.2650.21779
X-RAY DIFFRACTIONr_nbtor_refined0.310.22410
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3020.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.25
X-RAY DIFFRACTIONr_mcbond_it1.531.52229
X-RAY DIFFRACTIONr_mcangle_it1.49123493
X-RAY DIFFRACTIONr_scbond_it2.64231475
X-RAY DIFFRACTIONr_scangle_it3.9514.51302
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 65 -
Rwork0.224 1073 -
obs--100 %

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