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- PDB-1olo: Hexameric Replicative DNA Helicase RepA from Plasmid RSF1010 - Cu... -

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Basic information

Entry
Database: PDB / ID: 1olo
TitleHexameric Replicative DNA Helicase RepA from Plasmid RSF1010 - Cubic Crystal Structure
ComponentsREGULATORY PROTEIN REPA
KeywordsTRANSCRIPTION / DNA HELICASE / ATPASE / MOTOR PROTEIN
Function / homology
Function and homology information


plasmid maintenance / ATP binding
Similarity search - Function
Regulatory protein RepA / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Regulatory protein RepA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.55 Å
AuthorsNiedenzu, T. / Saenger, W.
CitationJournal: Nucleic Acids Res. / Year: 2003
Title: Hexameric Rsf1010 Helicase Repa: The Structural and Functional Importance of Single Amino Acid Residues
Authors: Ziegelin, G. / Niedenzu, T. / Lurz, R. / Saenger, W. / Lanka, E.
History
DepositionAug 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: REGULATORY PROTEIN REPA
B: REGULATORY PROTEIN REPA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0834
Polymers59,8902
Non-polymers1922
Water7,584421
1
A: REGULATORY PROTEIN REPA
B: REGULATORY PROTEIN REPA
hetero molecules

A: REGULATORY PROTEIN REPA
B: REGULATORY PROTEIN REPA
hetero molecules

A: REGULATORY PROTEIN REPA
B: 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 operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area21590 Å2
ΔGint-228.4 kcal/mol
Surface area58140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.293, 190.293, 190.293
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-2016-

HOH

DetailsTHE ASSEMBLY DESCRIBED BELOW IS A HOMOHEXAMERIC ASSEMBLY.

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Components

#1: Protein REGULATORY PROTEIN REPA


Mass: 29945.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Description: BROAD HOST RANGE PLASMID RSF1010 / Plasmid: PTACREP-A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P20356
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 4.8 Å3/Da / Density % sol: 74.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: SITTING DROP VAPOR DIFFUSION AT 291K. PROTEIN STOCK: 26MG/ML REPA, 10MM TRIS-HCL PH8.0, 150MM NACL, 0.1MM EDTA. PRECIPITANT: 100MM TRIS-HCL PH 7.5, 26% PEG400, 100MM MGSO4
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
126 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
3150 mM1dropNaCl
40.1 mMEDTA1drop
5100 mMTris-HCl1reservoirpH7.5
626 %PEG4001reservoir
7100 mM1reservoirMgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 2000 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.52→150 Å / Num. obs: 40046 / % possible obs: 99.1 % / Redundancy: 7.64 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 13.6
Reflection shellResolution: 2.52→2.58 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.3 / % possible all: 89.7
Reflection
*PLUS
Highest resolution: 2.52 Å / Num. measured all: 305969 / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1G8Y

1g8y


Resolution: 2.55→25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.671 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.211 991 2.6 %RANDOM
Rwork0.176 ---
obs-37753 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 34.09 Å2
Refinement stepCycle: LAST / Resolution: 2.55→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 10 421 4241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8291.52490
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56423987
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.63331475
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2234.51402
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.302 69
Rwork0.23 2726
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8844-1.4067-0.24382.2839-0.48711.21970.1370.189-0.485-0.2166-0.16270.3090.1982-0.03540.02570.08580.0558-0.02290.0722-0.06980.090116.011446.123761.3307
22.3847-1.2559-0.47011.8448-0.17181.66910.03110.2764-0.2422-0.1380.02490.27640.1909-0.4859-0.0560.0668-0.0144-0.07410.20940.02630.087436.271721.460565.9339
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 270
2X-RAY DIFFRACTION1A300
3X-RAY DIFFRACTION2B2 - 271
4X-RAY DIFFRACTION2B300
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 2.6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.838

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