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- PDB-2fwr: Structure of Archaeoglobus Fulgidis XPB -

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Basic information

Entry
Database: PDB / ID: 2fwr
TitleStructure of Archaeoglobus Fulgidis XPB
ComponentsDNA repair protein RAD25
KeywordsDNA BINDING PROTEIN / DNA Unwinding / DNA Repair / XPB
Function / homology
Function and homology information


DNA 3'-5' helicase / transcription preinitiation complex / 3'-5' DNA helicase activity / transcription initiation at RNA polymerase II promoter / hydrolase activity / DNA binding / ATP binding
Similarity search - Function
MutS, DNA mismatch repair protein, domain I - #30 / Xeroderma pigmentosum group B helicase, damage recognition domain / Xeroderma pigmentosum group B helicase damage recognition domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / MutS, DNA mismatch repair protein, domain I / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. ...MutS, DNA mismatch repair protein, domain I - #30 / Xeroderma pigmentosum group B helicase, damage recognition domain / Xeroderma pigmentosum group B helicase damage recognition domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / MutS, DNA mismatch repair protein, domain I / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / PHOSPHATE ION / DNA 3'-5' translocase XPB
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFan, L. / Arvai, A.S. / Tainer, J.A.
CitationJournal: Mol.Cell / Year: 2006
Title: Conserved XPB Core Structure and Motifs for DNA Unwinding: Implications for Pathway Selection of Transcription or Excision Repair
Authors: Fan, L. / Arvai, A.S. / Cooper, P.K. / Iwai, S. / Hanaoka, F. / Tainer, J.A.
History
DepositionFeb 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein RAD25
B: DNA repair protein RAD25
C: DNA repair protein RAD25
D: DNA repair protein RAD25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,03515
Polymers216,0954
Non-polymers94011
Water19,2041066
1
A: DNA repair protein RAD25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2995
Polymers54,0241
Non-polymers2754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA repair protein RAD25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3094
Polymers54,0241
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA repair protein RAD25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1192
Polymers54,0241
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA repair protein RAD25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3094
Polymers54,0241
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.085, 97.963, 113.731
Angle α, β, γ (deg.)79.03, 85.54, 89.69
Int Tables number1
Space group name H-MP1
DetailsThe asymetric unit contains 4 biological units (chains A,B,C,D).

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Components

#1: Protein
DNA repair protein RAD25


Mass: 54023.816 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: PET-28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29889
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1066 / 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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: TRIS/HCL, PEG 20K, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 57207 / Num. obs: 57207 / % possible obs: 88.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.094 / Χ2: 1.038 / Net I/σ(I): 9.9
Reflection shellResolution: 2.6→2.69 Å / % possible obs: 51.1 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.405 / Num. unique obs: 3271 / Χ2: 0.667 / % possible all: 51.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT1.701data extraction
ADSCdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.35 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 457366.125 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3 2735 5.1 %RANDOM
Rwork0.237 ---
all0.221 54080 --
obs0.221 54080 84.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 97.511 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso mean: 63.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.41 Å2-0.22 Å2-1.06 Å2
2--4.78 Å2-3.72 Å2
3----1.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13651 0 40 1078 14769
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.592
X-RAY DIFFRACTIONc_scbond_it1.612
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 264 4.9 %
Rwork0.315 5114 -
obs-5378 50.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ioh.parioh.top

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