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- PDB-2vsf: Structure of XPD from Thermoplasma acidophilum -

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Basic information

Entry
Database: PDB / ID: 2vsf
TitleStructure of XPD from Thermoplasma acidophilum
ComponentsDNA REPAIR HELICASE RAD3 RELATED PROTEIN
KeywordsHYDROLASE / NER / TFIIH / HELICASE / ATP-BINDING / NUCLEOTIDE-BINDING / IRON SULFUR CLUSTER
Function / homology
Function and homology information


DNA 5'-3' helicase / isomerase activity / 4 iron, 4 sulfur cluster binding / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA repair / ATP hydrolysis activity / DNA binding ...DNA 5'-3' helicase / isomerase activity / 4 iron, 4 sulfur cluster binding / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Fumarase C; Chain B, domain 1 - #40 / Bacterial XPD DNA helicase, FeS cluster domain / Bacterial type XPD DNA helicase, FeS cluster domain / DNA Binding (I), subunit A / Helical and beta-bridge domain / Helical and beta-bridge domain / Fumarase C; Chain B, domain 1 / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 ...Fumarase C; Chain B, domain 1 - #40 / Bacterial XPD DNA helicase, FeS cluster domain / Bacterial type XPD DNA helicase, FeS cluster domain / DNA Binding (I), subunit A / Helical and beta-bridge domain / Helical and beta-bridge domain / 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. / Superfamilies 1 and 2 helicase C-terminal domain profile. / 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
IRON/SULFUR CLUSTER / ATP-dependent DNA helicase XPD
Similarity search - Component
Biological speciesTHERMOPLASMA ACIDOPHILUM (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsKuper, J. / Wolski, S.C. / Truglio, J.J. / Kisker, C.
CitationJournal: Plos Biol. / Year: 2008
Title: Crystal Structure of the Fes Cluster-Containing Nucleotide Excision Repair Helicase Xpd.
Authors: Wolski, S.C. / Kuper, J. / Haenzelmann, P. / Truglio, J.J. / Croteau, D.L. / Van Houten, B. / Kisker, C.
History
DepositionApr 23, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA REPAIR HELICASE RAD3 RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6523
Polymers69,2601
Non-polymers3922
Water181
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.890, 78.890, 174.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein DNA REPAIR HELICASE RAD3 RELATED PROTEIN / XPD


Mass: 69260.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOPLASMA ACIDOPHILUM (acidophilic) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HM14
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.17 Å3/Da / Density % sol: 43.4 % / Description: NONE
Crystal growDetails: 0.2M MGCL2, 10-15% PEG 400, 0.1M SODIUM CITRATE PH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→63.63 Å / Num. obs: 13622 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.98 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.89
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.24 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.895 / SU B: 49.724 / SU ML: 0.427 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.515 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 657 4.9 %RANDOM
Rwork0.206 ---
obs0.209 12870 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: 54.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.08 Å20 Å2
2---0.15 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4751 0 9 1 4761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224857
X-RAY DIFFRACTIONr_bond_other_d0.0010.023452
X-RAY DIFFRACTIONr_angle_refined_deg0.9251.9766540
X-RAY DIFFRACTIONr_angle_other_deg0.7838354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81323.432236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61215899
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2611542
X-RAY DIFFRACTIONr_chiral_restr0.0550.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025356
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021032
X-RAY DIFFRACTIONr_nbd_refined0.2010.21229
X-RAY DIFFRACTIONr_nbd_other0.1680.23652
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22381
X-RAY DIFFRACTIONr_nbtor_other0.0810.22692
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1370.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.79123061
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4744727
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.90352086
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.97981801
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: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.319 64
Rwork0.319 895
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)
14.065-0.0917-0.299910.1864-3.69554.7998-0.03660.60670.0755-1.52070.43521.63550.668-0.6454-0.3985-0.0085-0.2876-0.2840.02610.09850.1749-44.735834.132812.3891
22.30951.7334-1.10877.3572-1.91838.09340.19210.04410.3662-0.20680.25560.7117-0.1386-0.2338-0.4477-0.21120.0160.0614-0.20520.0859-0.0837-35.618457.120913.1739
32.6264-1.52180.98958.79061.29862.2422-0.065-0.3632-0.06430.36740.2718-0.24690.23870.1581-0.2068-0.3212-0.08860.07780.0944-0.0536-0.2142-26.323542.00642.0677
45.4153-0.5369-3.22510.97352.70118.0828-0.12350.32990.1845-0.08080.2391-0.2384-0.54180.5905-0.11560.3091-0.145-0.0594-0.00020.00420.1553-22.103917.90949.1766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 79
2X-RAY DIFFRACTION1A176 - 224
3X-RAY DIFFRACTION1A363 - 405
4X-RAY DIFFRACTION2A80 - 175
5X-RAY DIFFRACTION2A1616
6X-RAY DIFFRACTION3A225 - 362
7X-RAY DIFFRACTION4A406 - 615

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