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- PDB-1qhh: STRUCTURE OF DNA HELICASE WITH ADPNP -

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Basic information

Entry
Database: PDB / ID: 1qhh
TitleSTRUCTURE OF DNA HELICASE WITH ADPNP
Components(PROTEIN (PCRA ...) x 4
KeywordsHYDROLASE / DNA REPAIR / DNA REPLICATION / SOS RESPONSE / HELICASE / ATP-BINDING / DNA-BINDING
Function / homology
Function and homology information


DNA 3'-5' helicase / DNA unwinding involved in DNA replication / isomerase activity / DNA helicase activity / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Double Stranded RNA Binding Domain - #800 / ATP-dependent DNA helicase PcrA / PcrA/UvrD tudor domain / PCRA; domain 4 / PCRA; domain 4 / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain ...Double Stranded RNA Binding Domain - #800 / ATP-dependent DNA helicase PcrA / PcrA/UvrD tudor domain / PCRA; domain 4 / PCRA; domain 4 / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like helicase, ATP-binding domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / Double Stranded RNA Binding Domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ATP-dependent DNA helicase PcrA
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSoultanas, P. / Dillingham, M.S. / Velankar, S.S. / Wigley, D.B.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: DNA binding mediates conformational changes and metal ion coordination in the active site of PcrA helicase.
Authors: Soultanas, P. / Dillingham, M.S. / Velankar, S.S. / Wigley, D.B.
History
DepositionMay 14, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jul 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (PCRA (SUBUNIT))
B: PROTEIN (PCRA (SUBUNIT))
C: PROTEIN (PCRA (SUBUNIT))
D: PROTEIN (PCRA (SUBUNIT))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1565
Polymers82,6494
Non-polymers5071
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21010 Å2
ΔGint-130 kcal/mol
Surface area27600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.936, 138.936, 111.642
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 (PCRA ... , 4 types, 4 molecules ABCD

#1: Protein PROTEIN (PCRA (SUBUNIT))


Mass: 18850.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: NCA1503 / Gene: PCRA / Plasmid: PET22 / Gene (production host): PCRA / Production host: Escherichia coli (E. coli) / References: UniProt: P56255
#2: Protein PROTEIN (PCRA (SUBUNIT))


Mass: 32419.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: NCA1503 / Gene: PCRA / Plasmid: PET22 / Gene (production host): PCRA / Production host: Escherichia coli (E. coli) / References: UniProt: P56255
#3: Protein PROTEIN (PCRA (SUBUNIT))


Mass: 12821.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: NCA1503 / Gene: PCRA / Plasmid: PET22 / Gene (production host): PCRA / Production host: Escherichia coli (E. coli) / References: UniProt: P56255
#4: Protein PROTEIN (PCRA (SUBUNIT))


Mass: 18557.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: NCA1503 / Gene: PCRA / Plasmid: PET22 / Gene (production host): PCRA / Production host: Escherichia coli (E. coli) / References: UniProt: P56255

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Non-polymers , 2 types, 95 molecules

#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.76 Å3/Da / Density % sol: 67.31 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Bird, L.E., (1998) Nucl. Acids Res., 26, 2686.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMTris1drop
3300 mM1dropNaCl
4100 mMMES1reservoir
51.0 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Type: SRS / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. obs: 42105 / % possible obs: 92.5 % / Observed criterion σ(I): 0 / Redundancy: 2.36 % / Rmerge(I) obs: 0.103

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.285 --
Rwork0.228 --
obs-37802 92.5 %
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5166 0 31 94 5291
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.047
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / σ(F): 0 / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS

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