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- PDB-1nlf: Crystal Structure of DNA Helicase RepA in complex with sulfate at... -

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Basic information

Entry
Database: PDB / ID: 1nlf
TitleCrystal Structure of DNA Helicase RepA in complex with sulfate at 1.95 A resolution
ComponentsRegulatory protein repA
KeywordsREPLICATION / replicative DNA helicase structural changes
Function / homology
Function and homology information


plasmid maintenance / ATP binding
Similarity search - Function
Regulatory protein RepA / AAA 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
Regulatory protein RepA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsXu, H. / Strater, N. / Schroeder, W. / Bottcher, C. / Ludwig, K. / Saenger, W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of DNA helicase RepA in complex with sulfate at 1.95 A resolution implicates structural changes to an "open" form.
Authors: Xu, H. / Strater, N. / Schroder, W. / Bottcher, C. / Ludwig, K. / Saenger, W.
History
DepositionJan 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
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_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

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Assembly

Deposited unit
A: Regulatory protein repA
B: Regulatory protein repA
C: Regulatory protein repA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1246
Polymers89,8363
Non-polymers2883
Water13,619756
1
A: Regulatory protein repA
B: Regulatory protein repA
C: Regulatory protein repA
hetero molecules

A: Regulatory protein repA
B: Regulatory protein repA
C: Regulatory protein repA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,24812
Polymers179,6716
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area18300 Å2
ΔGint-198 kcal/mol
Surface area63880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)192.3, 55.3, 105.6
Angle α, β, γ (deg.)90.0, 122.9, 90.0
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the crystallographic 2-fold rotation axes parallel to b and stacked face-to-face in a and c directions.

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Components

#1: Protein Regulatory protein repA


Mass: 29945.189 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: REPA / Plasmid: pMS119EH / Production host: Escherichia coli (E. coli) / Strain (production host): pGZ18 / References: UniProt: P20356
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 756 / 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: 2.56 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, TRIS buffer, magnesium sulfate , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 277 K / pH: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
117 mg/mlprotein1drop
240 mMMES/NaOH1droppH5.8
310 mM1dropMgCl2
480 mM1dropNaCl
51 mMAMP-PNP1drop
6100000 mM(dT)121drop
7200 mM1reservoirMgSO4
8100 mMTris-Cl1reservoirpH8.0
928 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.83432 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 18, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.83432 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 87437 / Num. obs: 72794 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 243785
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 6.8

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→20 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 6566 -RANDOM
Rwork0.201 ---
all0.236 68262 --
obs0.212 64722 94.8 %-
Displacement parametersBiso mean: 21.4 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5805 0 15 756 6576
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.23
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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