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- PDB-2vl7: Structure of S. tokodaii Xpd4 -

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Basic information

Entry
Database: PDB / ID: 2vl7
TitleStructure of S. tokodaii Xpd4
ComponentsXPD
KeywordsUNKNOWN FUNCTION / HELICASE
Function / homology
Function and homology information


DNA conformation change / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / isomerase activity / 4 iron, 4 sulfur cluster binding / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA repair ...DNA conformation change / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / isomerase activity / 4 iron, 4 sulfur cluster binding / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA repair / DNA binding / ATP binding / metal ion binding
Similarity search - Function
: / DNA repair helicase XPD, arch domain / Fumarase C; Chain B, domain 1 - #30 / Fumarase C; Chain B, domain 1 / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / HELICc2 ...: / DNA repair helicase XPD, arch domain / Fumarase C; Chain B, domain 1 - #30 / Fumarase C; Chain B, domain 1 / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / HELICc2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA repair helicase XPD
Similarity search - Component
Biological speciesSULFOLOBUS TOKODAII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.25 Å
AuthorsNaismith, J.H. / Johnson, K.A. / Oke, M. / McMahon, S.A. / Liu, L. / White, M.F. / Zawadski, M. / Carter, L.G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structure of the DNA Repair Helicase Xpd.
Authors: Liu, L. / Johnson, K.A. / Rudolf, J. / Mcrobbie, A.-M. / Mcmahon, S.A. / Oke, M. / Carter, L.G. / Naismith, J.H. / White, M.F.
History
DepositionJan 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4212
Polymers62,3261
Non-polymers951
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.713, 100.294, 62.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein XPD / UNCHARACTERIZED PROTEIN ST1307


Mass: 62326.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS TOKODAII (archaea) / Strain: 7 / Plasmid: PET DERIVED / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q971R4
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.14 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.06
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 2.25→29.7 Å / Num. obs: 27650 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.2
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.25→29.7 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.109 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1472 5.1 %RANDOM
Rwork0.232 ---
obs0.234 27650 99.7 %-
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: 54.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20 Å2
2---1.57 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 5 73 3790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223776
X-RAY DIFFRACTIONr_bond_other_d0.0040.022673
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.9995081
X-RAY DIFFRACTIONr_angle_other_deg1.0163.0026540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0465455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38824.125160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42915761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5761525
X-RAY DIFFRACTIONr_chiral_restr0.0920.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024021
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02718
X-RAY DIFFRACTIONr_nbd_refined0.2070.2747
X-RAY DIFFRACTIONr_nbd_other0.1770.22674
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21796
X-RAY DIFFRACTIONr_nbtor_other0.0830.22048
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2114
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0920.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8211.53021
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92223712
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.26131742
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8274.51369
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.329 102
Rwork0.287 1952
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)
17.4634-2.53631.45823.9048-0.6822.6797-0.5627-0.77511.11510.49280.1772-0.6302-0.7531-0.22770.3855-0.10370.085-0.0693-0.1543-0.1156-0.0189-11.03925.87821.883
25.3958-0.68152.29922.8928-0.72467.65860.3213-0.41180.34690.67130.0884-0.3857-0.54820.8248-0.4097-0.1546-0.1385-0.0256-0.1352-0.1425-0.055817.3343.8827.843
35.65782.4016-3.84373.6318-2.24153.61390.41590.12351.1140.27530.25670.3963-0.6755-0.0229-0.6727-0.158-0.09560.0602-0.13750.0342-0.02886.8629.302-1.333
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 196
2X-RAY DIFFRACTION1A308 - 348
3X-RAY DIFFRACTION1A1541
4X-RAY DIFFRACTION2A197 - 307
5X-RAY DIFFRACTION3A349 - 540

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