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- PDB-6dcr: E. coli PriA helicase winged helix domain deletion protein -

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Basic information

Entry
Database: PDB / ID: 6dcr
TitleE. coli PriA helicase winged helix domain deletion protein
ComponentsPrimosomal protein N'
KeywordsDNA BINDING PROTEIN / PriA / Helicase / DNA replication restart
Function / homology
Function and homology information


DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / plasmid maintenance / primosome complex / DNA replication, synthesis of primer / 3'-5' DNA helicase activity / DNA unwinding involved in DNA replication / replication fork processing / DNA replication initiation / helicase activity ...DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / plasmid maintenance / primosome complex / DNA replication, synthesis of primer / 3'-5' DNA helicase activity / DNA unwinding involved in DNA replication / replication fork processing / DNA replication initiation / helicase activity / response to gamma radiation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA-templated DNA replication / double-strand break repair / DNA recombination / DNA replication / hydrolase activity / response to antibiotic / DNA binding / zinc ion binding / ATP binding
Similarity search - Function
: / Primosomal protein N'-like, winged helix / Primosomal protein N' / PriA DNA helicase, Cys-rich region (CRR) domain / Primosomal protein N', 3' DNA-binding domain / Primosomal protein N, C-terminal domain / Primosomal protein N', 3' DNA-binding domain superfamily / 3'DNA-binding domain (3'BD) / Primosomal protein N C-terminal domain / PriA DNA helicase Cys-rich region (CRR) domain ...: / Primosomal protein N'-like, winged helix / Primosomal protein N' / PriA DNA helicase, Cys-rich region (CRR) domain / Primosomal protein N', 3' DNA-binding domain / Primosomal protein N, C-terminal domain / Primosomal protein N', 3' DNA-binding domain superfamily / 3'DNA-binding domain (3'BD) / Primosomal protein N C-terminal domain / PriA DNA helicase Cys-rich region (CRR) domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Primosomal protein N'
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.978 Å
AuthorsSatyshur, K.A. / Windgassen, T.A. / Keck, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM098885 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase.
Authors: Windgassen, T.A. / Leroux, M. / Satyshur, K.A. / Sandler, S.J. / Keck, J.L.
History
DepositionMay 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Primosomal protein N'
B: Primosomal protein N'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,59514
Polymers154,5652
Non-polymers1,03012
Water7,422412
1
A: Primosomal protein N'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8948
Polymers77,2831
Non-polymers6117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Primosomal protein N'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7026
Polymers77,2831
Non-polymers4195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.132, 56.505, 195.863
Angle α, β, γ (deg.)90.00, 97.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Primosomal protein N' / ATP-dependent helicase PriA / Replication factor Y


Mass: 77282.500 Da / Num. of mol.: 2 / Mutation: delta 114-174
Source method: isolated from a genetically manipulated source
Details: deletion of the winged helix domain (114-174)
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: priA, b3935, JW3906 / Plasmid: pET15b-EcoliPriA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
References: UniProt: P17888, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
Description: Thin square sheets. Formed within one day and collected/froze after the second day.
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM HEPES-HCl pH 7.5, 9.5 % PEG 4000, 4 % Isopropanol, 8 % glycerol, 50 mM sodium malonate, and 25-100 mM sodium fluoride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12712 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12712 Å / Relative weight: 1
ReflectionResolution: 1.978→48.832 Å / Num. obs: 101849 / % possible obs: 96.75 % / Redundancy: 3.7 % / Biso Wilson estimate: 47.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05904 / Rpim(I) all: 0.03598 / Rrim(I) all: 0.06941 / Net I/σ(I): 11.18
Reflection shellResolution: 1.978→2.049 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.299 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 9857 / CC1/2: 0.374 / Rpim(I) all: 0.7657 / Rrim(I) all: 1.513 / % possible all: 94.98

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NL4 removing the winged helix domain

4nl4


Resolution: 1.978→48.832 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 5084 4.99 %
Rwork0.1856 --
obs0.1871 101832 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.978→48.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9390 0 44 412 9846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129750
X-RAY DIFFRACTIONf_angle_d1.17713310
X-RAY DIFFRACTIONf_dihedral_angle_d14.9225782
X-RAY DIFFRACTIONf_chiral_restr0.0591540
X-RAY DIFFRACTIONf_plane_restr0.0071715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9781-2.00060.39861480.36882921X-RAY DIFFRACTION90
2.0006-2.02410.33891670.31843302X-RAY DIFFRACTION97
2.0241-2.04880.3441840.29683135X-RAY DIFFRACTION97
2.0488-2.07470.32151500.29093263X-RAY DIFFRACTION97
2.0747-2.1020.29261770.26843218X-RAY DIFFRACTION97
2.102-2.13080.25981620.25883159X-RAY DIFFRACTION97
2.1308-2.16120.2861730.23943229X-RAY DIFFRACTION96
2.1612-2.19350.27321690.23553156X-RAY DIFFRACTION97
2.1935-2.22780.24981750.22843233X-RAY DIFFRACTION97
2.2278-2.26430.26711720.2263212X-RAY DIFFRACTION97
2.2643-2.30330.25251540.21913215X-RAY DIFFRACTION97
2.3033-2.34520.27941700.2033171X-RAY DIFFRACTION96
2.3452-2.39030.23611570.19872910X-RAY DIFFRACTION88
2.3903-2.43910.20531600.18543233X-RAY DIFFRACTION97
2.4391-2.49220.23431660.18213293X-RAY DIFFRACTION99
2.4922-2.55010.22771790.18353302X-RAY DIFFRACTION99
2.5501-2.61390.23411780.17753260X-RAY DIFFRACTION99
2.6139-2.68460.20791670.17763310X-RAY DIFFRACTION99
2.6846-2.76360.20611810.17913256X-RAY DIFFRACTION99
2.7636-2.85270.23631630.18293277X-RAY DIFFRACTION99
2.8527-2.95470.2031800.17653298X-RAY DIFFRACTION98
2.9547-3.0730.22511650.17883279X-RAY DIFFRACTION99
3.073-3.21280.21991740.17423277X-RAY DIFFRACTION98
3.2128-3.38220.20571740.17733294X-RAY DIFFRACTION98
3.3822-3.5940.20561720.16353288X-RAY DIFFRACTION98
3.594-3.87140.18971770.16493287X-RAY DIFFRACTION98
3.8714-4.26080.18881740.15753235X-RAY DIFFRACTION96
4.2608-4.87680.16431630.15033028X-RAY DIFFRACTION90
4.8768-6.14240.211780.19063382X-RAY DIFFRACTION99
6.1424-48.84690.23061750.21483325X-RAY DIFFRACTION94
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)
12.63190.4349-1.29551.7158-0.62052.8691-0.1568-0.20920.05730.14150.182-0.128-0.1920.015-0.0220.36040.0288-0.00120.1433-0.02140.386632.23162.6228198.5389
22.63180.67190.6111.16760.08283.1597-0.27660.4276-0.2929-0.32750.2583-0.16120.46310.0893-0.01140.4617-0.07770.11290.2402-0.06320.438244.85094.4681174.8327
36.8352-2.0263-1.56492.42190.9383.0583-0.014-0.0931-0.4875-0.02170.09760.20160.6330.0544-0.06580.6037-0.1556-0.08170.5898-0.06470.391820.5273-15.9528151.934
46.107-0.25-0.35735.67170.22417.58330.0145-0.5631-0.72480.79680.3551-0.48240.92791.2285-0.41230.85590.2588-0.13951.073-0.08040.722240.0823-21.4742159.7858
53.1840.5769-0.79971.76050.53253.2737-0.02520.22560.0731-0.08330.06390.0949-0.17150.1842-0.04220.3632-0.1235-0.10040.34130.04540.346420.2431-1.7817166.896
63.6422-1.15330.71422.8079-0.01852.78780.14750.1414-0.0473-0.14730.14780.50430.1074-0.6901-0.29480.5322-0.0934-0.05481.24420.13590.568545.99-3.1334103.3513
73.6891-1.05441.65172.8319-0.60024.57370.01230.54150.41570.02610.0106-0.3807-0.21510.3003-0.03870.4513-0.10740.011.13290.00290.560171.533-6.5475107.1253
81.574-0.7921-0.54421.1466-0.08656.4282-0.12520.25160.7262-0.05570.1764-0.0222-0.7483-0.1173-0.01840.76-0.1585-0.20050.7936-0.030.920178.372410.8553138.8535
93.85340.04270.39781.6630.19362.1420.01760.17350.18860.0307-0.0577-0.1102-0.35780.1001-0.00270.6748-0.1788-0.10410.89070.020.440873.8971-1.3076132.9771
106.0182-1.3429-1.22128.01760.3274.2581-0.12590.1546-0.10520.39720.03340.9526-0.6921-0.72340.22580.6776-0.0772-0.02351.1598-0.00490.596248.9089-6.2031132.3067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 198 )
2X-RAY DIFFRACTION2chain 'A' and (resid 199 through 390 )
3X-RAY DIFFRACTION3chain 'A' and (resid 391 through 495 )
4X-RAY DIFFRACTION4chain 'A' and (resid 496 through 554 )
5X-RAY DIFFRACTION5chain 'A' and (resid 555 through 731 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 198 )
7X-RAY DIFFRACTION7chain 'B' and (resid 199 through 377 )
8X-RAY DIFFRACTION8chain 'B' and (resid 378 through 566 )
9X-RAY DIFFRACTION9chain 'B' and (resid 567 through 653 )
10X-RAY DIFFRACTION10chain 'B' and (resid 654 through 730 )

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