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- PDB-2d7e: Crystal structure of N-terminal domain of PriA from E.coli -

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Basic information

Entry
Database: PDB / ID: 2d7e
TitleCrystal structure of N-terminal domain of PriA from E.coli
ComponentsPrimosomal protein N'
KeywordsHYDROLASE / inter-twined
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 / response to gamma radiation ...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 / response to gamma radiation / helicase activity / 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
PriA, 3(prime) DNA-binding domain / 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, 3(prime) DNA-binding domain / 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 / GIY-YIG endonuclease / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Primosomal protein N'
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsSasaki, K. / Ose, T. / Maenaka, K. / Masai, H. / Kohda, D.
Citation
Journal: EMBO J. / Year: 2007
Title: Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA.
Authors: Sasaki, K. / Ose, T. / Okamoto, N. / Maenaka, K. / Tanaka, T. / Masai, H. / Saito, M. / Shirai, T. / Kohda, D.
#1: Journal: Biochim.Biophys.Acta / Year: 2006
Title: Crystallization and preliminary crystallographic analysis of the N-terminal domain of PriA from Escherichia coli
Authors: Sasaki, K. / Ose, T. / Tanaka, T. / Mizukoshi, T. / Ishigaki, T. / Maenaka, K. / Masai, H. / Kohda, D.
History
DepositionNov 18, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 27, 2019Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Primosomal protein N'
B: Primosomal protein N'
C: Primosomal protein N'
D: Primosomal protein N'


Theoretical massNumber of molelcules
Total (without water)47,1074
Polymers47,1074
Non-polymers00
Water1,00956
1
A: Primosomal protein N'
B: Primosomal protein N'


Theoretical massNumber of molelcules
Total (without water)23,5542
Polymers23,5542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-24 kcal/mol
Surface area12560 Å2
MethodPISA
2
C: Primosomal protein N'
D: Primosomal protein N'


Theoretical massNumber of molelcules
Total (without water)23,5542
Polymers23,5542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-26 kcal/mol
Surface area12320 Å2
MethodPISA
3
A: Primosomal protein N'
B: Primosomal protein N'

A: Primosomal protein N'
B: Primosomal protein N'


Theoretical massNumber of molelcules
Total (without water)47,1074
Polymers47,1074
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
Buried area11610 Å2
ΔGint-79 kcal/mol
Surface area21590 Å2
MethodPISA
4
C: Primosomal protein N'
D: Primosomal protein N'

C: Primosomal protein N'
D: Primosomal protein N'


Theoretical massNumber of molelcules
Total (without water)47,1074
Polymers47,1074
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area12140 Å2
ΔGint-77 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.570, 111.570, 260.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 11776.790 Da / Num. of mol.: 4 / Fragment: DNA binding domein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: priA / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P17888, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1M sodium citrate, 0.3M ammonium sulfate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL12B211
SYNCHROTRONPhoton Factory BL-6A20.97899, 0.97957, 0.94000
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 6, 2005
ADSC QUAMTUM 4r2CCDJan 26, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.978991
30.979571
40.941
ReflectionResolution: 2.5→20 Å / Num. all: 21937 / Num. obs: 20806 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.55 % / Biso Wilson estimate: 72.19 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 38.4
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 7.5 / Num. unique all: 600 / % possible all: 94.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 3.5 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.2923 1418 -RANDOM
Rwork0.2472 ---
all-21937 --
obs-19914 90.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.207 Å2-4.267 Å20 Å2
2---2.766 Å20 Å2
3---2.973 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 0 56 3352
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0084
X-RAY DIFFRACTIONc_angle_deg1.485
X-RAY DIFFRACTIONc_dihedral_angle_d23.81
X-RAY DIFFRACTIONc_improper_angle_d1.14
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.3848 73 -
Rwork0.3234 --
obs-1267 58 %

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