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- PDB-5h8c: Truncated XPD -

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Basic information

Entry
Database: PDB / ID: 5h8c
TitleTruncated XPD
ComponentsXPD/Rad3 related DNA helicase
KeywordsHYDROLASE / helicase
Function / homology
Function and homology information


5'-3' DNA helicase activity / nucleobase-containing compound metabolic process / DNA duplex unwinding / DNA helicase activity / 4 iron, 4 sulfur cluster binding / DNA helicase / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Fumarase C; Chain B, domain 1 - #30 / Helicase superfamily 1/2, DinG/Rad3-like / Helicase-like, DEXD box c2 type / ATP-dependent helicase, C-terminal / DEAD2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD_2 / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2 ...Fumarase C; Chain B, domain 1 - #30 / Helicase superfamily 1/2, DinG/Rad3-like / Helicase-like, DEXD box c2 type / ATP-dependent helicase, C-terminal / DEAD2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD_2 / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2 / HELICc2 / Fumarase C; Chain B, domain 1 / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / XPD/Rad3 related DNA helicase / ATP-dependent DNA helicase Saci_0192
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.29 Å
AuthorsNaismith, J.H. / Constantinescu, D.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Mechanism of DNA loading by the DNA repair helicase XPD.
Authors: Constantinescu-Aruxandei, D. / Petrovic-Stojanovska, B. / Penedo, J.C. / White, M.F. / Naismith, J.H.
History
DepositionDec 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XPD/Rad3 related DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4382
Polymers64,0861
Non-polymers3521
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-21 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.800, 77.800, 99.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein XPD/Rad3 related DNA helicase / XPD helicase


Mass: 64086.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein degraded (domain clipped off) during crystallisation
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: SacN8_00920 / Production host: Escherichia coli (E. coli) / References: UniProt: M1J2P5, UniProt: Q4JC68*PLUS
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.4 / Details: PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.29→29 Å / Num. obs: 23154 / % possible obs: 99.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 18.2
Reflection shellResolution: 2.29→2.35 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementResolution: 2.29→29 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 14.512 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23912 1186 5.1 %RANDOM
Rwork0.20326 ---
obs0.20511 21920 99.43 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.675 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20 Å20 Å2
2--0.02 Å20 Å2
3---2.01 Å2
Refinement stepCycle: 1 / Resolution: 2.29→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 8 7 2765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192821
X-RAY DIFFRACTIONr_bond_other_d0.0010.022805
X-RAY DIFFRACTIONr_angle_refined_deg1.6762.0223841
X-RAY DIFFRACTIONr_angle_other_deg1.4173.0016485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8535333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48324.4125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2115560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3841517
X-RAY DIFFRACTIONr_chiral_restr0.0760.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02591
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5434.9081338
X-RAY DIFFRACTIONr_mcbond_other1.5424.9071337
X-RAY DIFFRACTIONr_mcangle_it2.547.3521669
X-RAY DIFFRACTIONr_mcangle_other2.5397.3531670
X-RAY DIFFRACTIONr_scbond_it1.9835.1761483
X-RAY DIFFRACTIONr_scbond_other1.9825.1761484
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0037.6512111
X-RAY DIFFRACTIONr_long_range_B_refined4.88137.5682961
X-RAY DIFFRACTIONr_long_range_B_other4.8837.5782962
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.292→2.351 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 89 -
Rwork0.303 1579 -
obs--99.7 %
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)
112.49631.9322-1.82063.54092.189310.8347-0.0117-0.9677-1.02130.9804-0.19850.57610.4637-0.90620.21020.53490.01290.04430.19330.13160.44610.2832.0695.626
28.3687-2.7924-0.65463.52260.39052.0564-0.0375-0.9172-0.5850.66850.14960.36710.00390.0237-0.11210.2602-0.05350.08460.11690.02940.2498-4.29518.1786.487
35.5865-1.4317-3.15653.6763-0.52169.14080.1164-0.2550.41540.2337-0.2860.0206-0.32840.60580.16960.2132-0.1051-0.00130.09060.0270.34611.9439.508-4.407
44.1565-0.5837-0.55435.7367-0.64042.8739-0.1539-0.34560.69690.4750.17310.0137-0.56740.023-0.01930.2599-0.04240.03790.071-0.1040.2328-3.0835.0743.32
54.3230.24650.14435.0058-0.09696.68550.23630.23590.3413-0.3689-0.2328-0.0414-0.29370.1724-0.00350.08480.03110.02840.03420.00010.15724.84818.899-7.018
62.92190.9225-1.54985.53562.80928.6711-0.16930.1572-0.0376-0.15590.0477-0.36010.49761.11230.12160.30130.0851-0.0340.28550.15290.323410.77335.172-31.881
72.23180.0009-1.42672.72810.35975.5967-0.0381-0.07310.069-0.3102-0.3089-0.04210.39440.57560.3470.39810.1152-0.03260.14480.14660.34637.30932.894-23.43
85.0436-1.43490.18353.63090.29434.56950.19250.1573-0.4011-0.1194-0.29190.24570.5239-0.27720.09940.1969-0.0121-0.03850.0389-0.03690.24396.1324.973-7.238
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 35
2X-RAY DIFFRACTION2A36 - 82
3X-RAY DIFFRACTION3A83 - 116
4X-RAY DIFFRACTION4A117 - 153
5X-RAY DIFFRACTION5A154 - 193
6X-RAY DIFFRACTION6A194 - 256
7X-RAY DIFFRACTION7A257 - 303
8X-RAY DIFFRACTION8A304 - 346

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