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- PDB-1fu1: CRYSTAL STRUCTURE OF HUMAN XRCC4 -

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Basic information

Entry
Database: PDB / ID: 1fu1
TitleCRYSTAL STRUCTURE OF HUMAN XRCC4
ComponentsDNA REPAIR PROTEIN XRCC4
KeywordsGENE REGULATION / helix-turn-helix / helix bundle
Function / homology
Function and homology information


FHA domain binding / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / immunoglobulin V(D)J recombination / protein localization to site of double-strand break / cellular response to lithium ion / 2-LTR circle formation ...FHA domain binding / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / immunoglobulin V(D)J recombination / protein localization to site of double-strand break / cellular response to lithium ion / 2-LTR circle formation / response to X-ray / SUMOylation of DNA damage response and repair proteins / Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / : / : / : / XRCC4 N-terminal domain / XRCC4 coiled-coil ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / : / : / : / XRCC4 N-terminal domain / XRCC4 coiled-coil / XRCC4 C-terminal region / XRCC4-like, N-terminal domain superfamily / DNA repair protein XRCC4-like, C-terminal / Beta Complex / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / DNA repair protein XRCC4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsJunop, M. / Modesti, M. / Guarne, A. / Gellert, M. / Yang, W.
CitationJournal: EMBO J. / Year: 2000
Title: Crystal structure of the Xrcc4 DNA repair protein and implications for end joining.
Authors: Junop, M.S. / Modesti, M. / Guarne, A. / Ghirlando, R. / Gellert, M. / Yang, W.
History
DepositionSep 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA REPAIR PROTEIN XRCC4
B: DNA REPAIR PROTEIN XRCC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8056
Polymers47,5652
Non-polymers2404
Water1,09961
1
A: DNA REPAIR PROTEIN XRCC4
B: DNA REPAIR PROTEIN XRCC4
hetero molecules

A: DNA REPAIR PROTEIN XRCC4
B: DNA REPAIR PROTEIN XRCC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,61012
Polymers95,1304
Non-polymers4808
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
2
A: DNA REPAIR PROTEIN XRCC4
B: DNA REPAIR PROTEIN XRCC4
hetero molecules

A: DNA REPAIR PROTEIN XRCC4
B: DNA REPAIR PROTEIN XRCC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,61012
Polymers95,1304
Non-polymers4808
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area12080 Å2
ΔGint-98 kcal/mol
Surface area41760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)164.892, 74.793, 87.307
Angle α, β, γ (deg.)90.00, 103.97, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
DetailsThe biological assembly is a tetramer constructed from chains A and B and their symmetry partners generated by a crystallographic two-fold

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Components

#1: Protein DNA REPAIR PROTEIN XRCC4


Mass: 23782.432 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-203 / Mutation: T135I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: NON-TISSUE SPECIFIC / Plasmid: PACYC154 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13426
#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium sulphate, magnesium acetate, DTT, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
2100 mMsodium cacodylate1reservoir
310 mMdithiothreitol1reservoir
41.2 Mammonium sulfate1reservoir
510 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 31958 / Num. obs: 31338 / % possible obs: 98.1 % / Observed criterion σ(I): 1.19 / Redundancy: 13.7 % / Biso Wilson estimate: 71.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.03
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.408 / Num. unique all: 1527 / % possible all: 95.9
Reflection shell
*PLUS
% possible obs: 95.9 % / Mean I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.7→29.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1150054.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood using intensities
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2791 9.9 %RANDOM
Rwork0.231 ---
all0.246 28110 --
obs0.246 28110 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 73.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.24 Å20 Å221.61 Å2
2--3.72 Å20 Å2
3---0.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 16 61 3177
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it3.731.5
X-RAY DIFFRACTIONc_mcangle_it5.82
X-RAY DIFFRACTIONc_scbond_it5.832
X-RAY DIFFRACTIONc_scangle_it8.432.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.411 468 10.2 %
Rwork0.388 4108 -
obs--96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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