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- PDB-1g8y: CRYSTAL STRUCTURE OF THE HEXAMERIC REPLICATIVE HELICASE REPA OF P... -

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Basic information

Entry
Database: PDB / ID: 1g8y
TitleCRYSTAL STRUCTURE OF THE HEXAMERIC REPLICATIVE HELICASE REPA OF PLASMID RSF1010
ComponentsREGULATORY PROTEIN REPA
KeywordsTRANSCRIPTION / P-loop
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 / MAD / Resolution: 2.4 Å
AuthorsNiedenzu, T. / Roeleke, D. / Bains, G. / Scherzinger, E. / Saenger, W.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of the hexameric replicative helicase RepA of plasmid RSF1010.
Authors: Niedenzu, T. / Roleke, D. / Bains, G. / Scherzinger, E. / Saenger, W.
History
DepositionNov 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REGULATORY PROTEIN REPA
B: REGULATORY PROTEIN REPA
C: REGULATORY PROTEIN REPA
D: REGULATORY PROTEIN REPA
E: REGULATORY PROTEIN REPA
F: REGULATORY PROTEIN REPA
G: REGULATORY PROTEIN REPA
H: REGULATORY PROTEIN REPA
I: REGULATORY PROTEIN REPA
J: REGULATORY PROTEIN REPA
K: REGULATORY PROTEIN REPA
L: REGULATORY PROTEIN REPA


Theoretical massNumber of molelcules
Total (without water)359,34212
Polymers359,34212
Non-polymers00
Water8,647480
1
A: REGULATORY PROTEIN REPA
B: REGULATORY PROTEIN REPA
C: REGULATORY PROTEIN REPA
D: REGULATORY PROTEIN REPA
E: REGULATORY PROTEIN REPA
F: REGULATORY PROTEIN REPA


Theoretical massNumber of molelcules
Total (without water)179,6716
Polymers179,6716
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18900 Å2
ΔGint-82 kcal/mol
Surface area54460 Å2
MethodPISA
2
G: REGULATORY PROTEIN REPA
H: REGULATORY PROTEIN REPA
I: REGULATORY PROTEIN REPA
J: REGULATORY PROTEIN REPA
K: REGULATORY PROTEIN REPA
L: REGULATORY PROTEIN REPA


Theoretical massNumber of molelcules
Total (without water)179,6716
Polymers179,6716
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18940 Å2
ΔGint-78 kcal/mol
Surface area54650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.432, 179.156, 116.289
Angle α, β, γ (deg.)90.00, 108.80, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsThe biological assembly is one of the two hexamers in the asymmetric unit: chains a-f or g-l

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Components

#1: Protein
REGULATORY PROTEIN REPA / REPLICATION PROTEIN A


Mass: 29945.189 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: REPA ON PLASMID INCQ RSF1010 / Plasmid: PTACREP-A / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P20356
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 5000 monomethyl ether, 2-methyl-2,4-pentanediol, NaCl, sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
138 mg/mlprotein1drop
210 mMTris-HCl1drop
310 mM1dropNa4P2O7
412 %(w/v)PEG5000 MME1reservoir
53 %(v/v)MPD1reservoir
6150 mM1reservoirNaCl
7100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9059 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 22, 1998
RadiationMonochromator: bent single-crystal germanium triangular monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9059 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 149192 / Num. obs: 149192 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.53 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 18.9
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 2.46 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 6.9 / Num. unique all: 8579 / % possible all: 81.7
Reflection
*PLUS
Num. measured all: 377676 / Rmerge(I) obs: 0.034
Reflection shell
*PLUS
% possible obs: 81.7 %

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2983 2.1 %SHELLS
Rwork0.221 ---
all-144837 --
obs-144837 92 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.8 Å20 Å27.59 Å2
2---13.36 Å20 Å2
3---19.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22056 0 0 480 22536
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.32 246 -
Rwork0.261 --
obs-11998 76 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 2.1 % / Rfactor obs: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.32 / Rfactor Rwork: 0.261

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