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- PDB-3crv: XPD_Helicase -

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Basic information

Entry
Database: PDB / ID: 3crv
TitleXPD_Helicase
ComponentsXPD/Rad3 related DNA helicase
KeywordsHYDROLASE / XPD Helicase DNA Repair Cancer Aging / Helicase
Function / homology
Function and homology information


5'-3' DNA helicase activity / DNA duplex unwinding / 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
CITRATE ANION / ISOPROPYL ALCOHOL / IRON/SULFUR CLUSTER / ATP-dependent DNA helicase Saci_0192
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsFan, L. / Arvai, A.S. / Tainer, J.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations.
Authors: Fan, L. / Fuss, J.O. / Cheng, Q.J. / Arvai, A.S. / Hammel, M. / Roberts, V.A. / Cooper, P.K. / Tainer, J.A.
History
DepositionApr 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 5, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity_src_gen / struct
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _struct.title
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,14011
Polymers64,0861
Non-polymers1,05310
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.542, 70.222, 144.293
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein XPD/Rad3 related DNA helicase


Mass: 64086.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: Saci_0192 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q4JC68, Hydrolases

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Non-polymers , 5 types, 269 molecules

#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.4M Citrate pH 5.6 15-20% PEG 4000 10% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.12710, 0.97931, 0.97899, 0.91837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 26, 2007
RadiationMonochromator: SSRL beamline 11-1 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.12711
20.979311
30.978991
40.918371
ReflectionResolution: 2→42.58 Å / Num. all: 37481 / Num. obs: 37102 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.2 Å2 / Limit h max: 26 / Limit h min: 0 / Limit k max: 35 / Limit k min: 0 / Limit l max: 72 / Limit l min: 0 / Observed criterion F max: 202396.95 / Observed criterion F min: 0.32
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.41 / % possible all: 97.1

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→42.58 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Cross-validation method: -> "throughout" Free R value test set selection criteria: -> "random" Number of non-hydrogen atoms used in refinement. Polymer 4505 Nonpolymer 55 Solvent 259 CNS ...Details: Cross-validation method: -> "throughout" Free R value test set selection criteria: -> "random" Number of non-hydrogen atoms used in refinement. Polymer 4505 Nonpolymer 55 Solvent 259 CNS Parameter files: CNS_TOPPAR/protein_rep.param CNS_TOPPAR/water.param flc.par ./par.fs4 ./sol.par CNS Topology files: CNS_TOPPAR/protein.top CNS_TOPPAR/carbohydrate.top sol.top top.fs4 flc.top
RfactorNum. reflection% reflectionSelection details
Rfree0.26 3498 10 %RANDOM
Rwork0.222 ---
all0.227 37481 --
obs0.227 35040 93.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 67.2777 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 85.65 Å2 / Biso mean: 42.92 Å2 / Biso min: 14.01 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å20 Å2
2---2.2 Å20 Å2
3----0.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.24 Å
Luzzati d res high-2
Refinement stepCycle: LAST / Resolution: 2→42.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4505 0 55 259 4819
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg22.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.78
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2-2.090.34740110.70.30533640.0174599376581.9
2.09-2.20.3123999.70.26437050.0164636410488.5
2.2-2.340.2844239.90.24338290.0144631425291.8
2.34-2.520.2844710.30.24439100.0134634435794
2.52-2.780.29447710.60.23540100.0134667448796.1
2.78-3.180.2874479.80.22940940.0144671454197.2
3.18-40.2114469.50.19942300.014735467698.8
4-42.580.2484589.40.2144000.0124937485898.4

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