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- PDB-2qm4: Crystal structure of human XLF/Cernunnos, a non-homologous end-jo... -

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Basic information

Entry
Database: PDB / ID: 2qm4
TitleCrystal structure of human XLF/Cernunnos, a non-homologous end-joining factor
ComponentsNon-homologous end-joining factor 1
KeywordsRECOMBINATION / XRCC4 like factor / homodimer / beta-sandwich / coiled-coil
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: 2.3 Å
AuthorsLi, Y. / Chirgadze, D.Y. / Sibanda, B.L. / Bolanos-Garcia, V.M. / Davies, O.R. / Blundell, T.L.
CitationJournal: Embo J. / Year: 2008
Title: Crystal structure of human XLF/Cernunnos reveals unexpected differences from XRCC4 with implications for NHEJ.
Authors: Li, Y. / Chirgadze, D.Y. / Bolanos-Garcia, V.M. / Sibanda, B.L. / Davies, O.R. / Ahnesorg, P. / Jackson, S.P. / Blundell, T.L.
History
DepositionJul 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)108,2394
Polymers108,2394
Non-polymers00
Water4,179232
1
A: Non-homologous end-joining factor 1
B: Non-homologous end-joining factor 1


Theoretical massNumber of molelcules
Total (without water)54,1202
Polymers54,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-58 kcal/mol
Surface area23010 Å2
MethodPISA, PQS
2
C: Non-homologous end-joining factor 1
D: Non-homologous end-joining factor 1


Theoretical massNumber of molelcules
Total (without water)54,1202
Polymers54,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-62 kcal/mol
Surface area22130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.736, 92.913, 103.693
Angle α, β, γ (deg.)90.00, 106.22, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer. Two dimers are present in the asymmetric unit of the crystal (chans A and B; chains C and D)

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Components

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


Mass: 27059.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NHEJ1, XLF / Plasmid: pETG-41A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q9H9Q4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 23% PEG 6000, 0.1M Bis-Tris-Propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9807 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2007
Details: toroidal mirror is curved by a pneumatically operated bending mechanism and focusses the beam in both the horizontal and vertica
RadiationMonochromator: Si(311) monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9807 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 51827 / Num. obs: 51723 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.302 / Num. unique all: 3438 / Rsym value: 0.0302 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ProDCdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→37.01 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.952 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.293 / ESU R Free: 0.225
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23891 2000 4.2 %RANDOM
Rwork0.18238 ---
all0.18478 45931 --
obs0.18478 45931 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.743 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0.02 Å2
2--0.14 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7113 0 0 232 7345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227447
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.97510136
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1345961
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12325.075333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.955151340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3731537
X-RAY DIFFRACTIONr_chiral_restr0.0940.21163
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025585
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.23009
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.290.24990
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2254
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.54354802
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.51267472
X-RAY DIFFRACTIONr_scbond_it3.17453018
X-RAY DIFFRACTIONr_scangle_it4.2457.52638
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 123 -
Rwork0.198 2832 -
obs-2955 100 %
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)
11.4269-0.07221.20850.82930.48936.14140.04470.04950.06890.0865-0.03660.03480.08320.0819-0.008-0.3297-0.00080.0242-0.2487-0.0194-0.297216.341.7738.645
26.13252.3652-5.6011.3153-2.46376.43660.1728-0.1399-0.00550.06610.01630.0534-0.297-0.1371-0.1891-0.22680.0291-0.0221-0.33970.0513-0.26664.75146.96942.689
32.28381.2433-2.91250.7323-1.79014.4696-0.2296-0.1532-0.3625-0.0238-0.1102-0.20430.11950.06760.3398-0.13320.0342-0.0288-0.34870.0364-0.15816.47439.19342.668
45.14180.73110.2572.68510.60261.28270.0125-0.72780.21290.2622-0.06250.15290.09490.06020.0501-0.28420.02170.0087-0.2162-0.0086-0.379436.88559.43942.109
57.65091.8467-4.74170.6055-1.14614.5467-0.3231-0.244-0.6965-0.09720.023-0.19740.4105-0.09820.3001-0.20030.01340.0136-0.37370.0749-0.186.98739.17341.745
65.2866-0.2702-1.5041.0251-1.1252.5940.1896-0.4260.2142-0.0788-0.006-0.0096-0.0458-0.0944-0.1837-0.2540.016-0.0105-0.35190.0252-0.32315.15247.32941.983
74.2266-1.0485-0.71092.1832-0.28452.550.07740.3699-0.1689-0.3519-0.09880.20690.2016-0.03130.0214-0.2421-0.0059-0.0102-0.2632-0.0388-0.379668.71835.544-19.002
813.0953-0.39067.87890.9832-0.34476.0243-0.4720.4951.41690.015-0.0537-0.152-0.4323-0.01430.5257-0.1017-0.04220.0447-0.25640.1083-0.069738.8156.512-18.035
95.29420.46852.90890.3656-0.15863.1165-0.02070.15680.0156-0.10750.03360.0257-0.02990.0327-0.0129-0.283-0.01890.0223-0.39040.0805-0.25635.15248.475-20.009
101.08020.4028-1.18661.0541.19526.8846-0.05670.22540.0209-0.17840.05310.0588-0.1909-0.06090.0036-0.25760.0018-0.0303-0.28240.0194-0.213248.9735214.82
115.0198-1.75822.20852.128-1.0211.19530.41780.51220.0326-0.2775-0.05140.21460.4720.2281-0.3664-0.2715-0.00590.0505-0.26270.0685-0.196936.53848.758-19.25
124.6072-0.18863.58080.4317-1.41736.5914-0.4230.36750.6278-0.23840.04140.0216-0.22920.16890.3816-0.1336-0.0230.0357-0.39650.0288-0.069338.74656.216-17.686
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 1261 - 128
2X-RAY DIFFRACTION2AA127 - 169129 - 171
3X-RAY DIFFRACTION3AA170 - 230172 - 232
4X-RAY DIFFRACTION4BB-1 - 1261 - 128
5X-RAY DIFFRACTION5BB127 - 169129 - 171
6X-RAY DIFFRACTION6BB174 - 227176 - 229
7X-RAY DIFFRACTION7CC-1 - 1261 - 128
8X-RAY DIFFRACTION8CC127 - 169129 - 171
9X-RAY DIFFRACTION9CC170 - 227172 - 229
10X-RAY DIFFRACTION10DD-1 - 1261 - 128
11X-RAY DIFFRACTION11DD127 - 169129 - 171
12X-RAY DIFFRACTION12DD170 - 229172 - 231

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