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- PDB-2fz4: Crystal Structure of the N-terminal half of Archaeoglobus Fulgidus XPB -

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Basic information

Entry
Database: PDB / ID: 2fz4
TitleCrystal Structure of the N-terminal half of Archaeoglobus Fulgidus XPB
ComponentsDNA repair protein RAD25
KeywordsDNA BINDING PROTEIN / RecA-like domain / DNA damage recognition domain
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
DNA 3'-5' translocase XPB
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsFan, L. / 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 9, 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: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA repair protein RAD25


Theoretical massNumber of molelcules
Total (without water)26,8261
Polymers26,8261
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.6, 117.6, 117.6
Angle α, β, γ (deg.)90, 90, 90
Int Tables number197
Space group name H-MI23

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Components

#1: Protein DNA repair protein RAD25


Mass: 26826.393 Da / Num. of mol.: 1 / Fragment: N-terminal half
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: RAD25 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29889
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.2
Details: 100 mM sodium citrate, 1.0 M LiCl., pH 5.2, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.98
SYNCHROTRONALS 5.0.220.9780, 0.9795, 0.9796
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDDec 14, 2002
ADSC QUANTUM 2102CCDJun 24, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.9781
30.97951
40.97961
ReflectionResolution: 2.4→40 Å / Num. obs: 10811 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 19.9 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 40.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 17.1 % / Mean I/σ(I) obs: 6.6 / Num. unique all: 1064 / Rsym value: 0.593 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.4→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 549 -random
Rwork0.2434 ---
all-10732 --
obs-10478 97.6 %-
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 0 39 1682

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