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- PDB-4a15: Crystal structure of an XPD DNA complex -

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Basic information

Entry
Database: PDB / ID: 4a15
TitleCrystal structure of an XPD DNA complex
Components
  • 5'-D(*DTP*AP*CP*GP)-3'
  • ATP-DEPENDENT DNA HELICASE TA0057
KeywordsHYDROLASE / HELICASE / NUCLEOTIDE EXCISION REPAIR
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 / DNA / ATP-dependent DNA helicase XPD
Similarity search - Component
Biological speciesTHERMOPLASMA ACIDOPHILUM (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKuper, J. / Wolski, S.C. / Michels, G. / Kisker, C.
CitationJournal: Embo J. / Year: 2011
Title: Functional and Structural Studies of the Nucleotide Excision Repair Helicase Xpd Suggest a Polarity for DNA Translocation.
Authors: Kuper, J. / Wolski, S.C. / Michels, G. / Kisker, C.
History
DepositionSep 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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.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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-DEPENDENT DNA HELICASE TA0057
E: 5'-D(*DTP*AP*CP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3467
Polymers72,6662
Non-polymers6805
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.060, 79.060, 175.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein / DNA chain , 2 types, 2 molecules AE

#1: Protein ATP-DEPENDENT DNA HELICASE TA0057 / XPD HELICASE


Mass: 71475.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOPLASMA ACIDOPHILUM (acidophilic) / Plasmid: PET16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9HM14, DNA helicase
#2: DNA chain 5'-D(*DTP*AP*CP*GP)-3'


Mass: 1190.830 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 139 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE NATIVE SEQUENCE IS REFERENCED TO THE NCBI DATABASE. THE DATABASE ACCESSION NUMBER IS NP_393536

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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: 2.2 Å3/Da / Density % sol: 43.4 % / Description: NONE
Crystal growDetails: 50 MM MES (PH 6.5), 10 MM MGSO4, 5-30% 2-METHYL-2 4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 92 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.972
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.2→52 Å / Num. obs: 30961 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VSF

2vsf


Resolution: 2.2→39.53 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 13.859 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25049 1545 5 %RANDOM
Rwork0.1923 ---
obs0.19524 29635 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.218 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.32 Å20 Å2
2--0.63 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4822 83 23 134 5062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195043
X-RAY DIFFRACTIONr_bond_other_d0.0010.023554
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.9726847
X-RAY DIFFRACTIONr_angle_other_deg1.34638602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6295595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07723.444241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.77115916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3511543
X-RAY DIFFRACTIONr_chiral_restr0.0880.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215484
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021071
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 101 -
Rwork0.259 2127 -
obs--97.34 %
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)
11.6273-0.6861-0.71892.40480.48311.82260.0695-0.03530.03580.22490.01460.0893-0.0964-0.0487-0.08410.07620.03040.03890.02820.00780.048-4.999334.627316.1094
21.3999-0.96370.05822.7666-0.45352.9475-0.05970.0090.01270.1010.08020.03060.2382-0.0005-0.02050.05430.00510.01950.01440.01340.06255.55839.564113.5137
31.05740.3256-0.39253.1293-0.30581.4987-0.01160.04950.0426-0.26550.0654-0.1241-0.01880.104-0.05380.0330.02410.0220.13260.03420.071814.872826.133-14.3937
42.98920.25810.08651.49950.38883.85770.027-0.32830.34960.1691-0.0348-0.26450.30070.51530.00780.2540.0510.05330.1127-0.03210.242518.451949.501419.6806
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 79
2X-RAY DIFFRACTION1A176 - 224
3X-RAY DIFFRACTION1A363 - 406
4X-RAY DIFFRACTION2A87 - 175
5X-RAY DIFFRACTION2A1616
6X-RAY DIFFRACTION3A225 - 362
7X-RAY DIFFRACTION4A407 - 615

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