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- PDB-6h8o: Crystal structure of the Master-Rep protein nuclease domain from ... -

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Basic information

Entry
Database: PDB / ID: 6h8o
TitleCrystal structure of the Master-Rep protein nuclease domain from the Faba Bean Necrotic Yellows Virus
ComponentsReplication-associated protein
KeywordsREPLICATION / endonuclease / Faba Bean Necrotic Yellows Virus / Rep protein / DNA replication
Function / homology
Function and homology information


: / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / RNA helicase activity / host cell nucleus / ATP hydrolysis activity ...: / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / RNA helicase activity / host cell nucleus / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / metal ion binding
Similarity search - Function
CRESS-DNA virus replication initiator protein (Rep) endonuclease domain profile. / Viral replication-associated protein, N-terminal / Putative viral replication protein / Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Replication-associated protein / Master replication protein
Similarity search - Component
Biological speciesFaba bean necrotic yellows virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å
AuthorsMoncalian, G. / Gonzalez-Montes, L.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-55534-C2-2-P Spain
CitationJournal: To Be Published
Title: Crystal structure of the Master-Rep protein nuclease domain from the Faba Bean Necrotic Yellows Virus
Authors: Moncalian, G. / Gonzalez-Montes, L.
History
DepositionAug 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 2.0Oct 3, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / refine / refine_ls_shell / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num / _refine_ls_shell.pdbx_refine_id / _struct_site_gen.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replication-associated protein
B: Replication-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,67810
Polymers21,9092
Non-polymers7698
Water5,224290
1
A: Replication-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2434
Polymers10,9551
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Replication-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4356
Polymers10,9551
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.230, 94.230, 45.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Replication-associated protein


Mass: 10954.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Faba bean necrotic yellows virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2D0XNJ4, UniProt: O39828*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium citrate tribasis dihydrate pH5.6, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.99989 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99989 Å / Relative weight: 1
ReflectionResolution: 1.15→47.115 Å / Num. obs: 81485 / % possible obs: 99.4 % / Redundancy: 15.4 % / Biso Wilson estimate: 11.36 Å2 / CC1/2: 0.997 / Net I/σ(I): 19.5
Reflection shellResolution: 1.15→1.21 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 5.6 / Num. unique obs: 11361 / CC1/2: 0.944 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLM7.2.2data reduction
SCALA3.3.21data scaling
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: SAD
Starting model: I3C

Resolution: 1.15→47.115 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.179 4125 -
Rwork0.1661 --
obs0.128 81452 99.32 %
Refinement stepCycle: LAST / Resolution: 1.15→47.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1534 0 40 290 1864
LS refinement shellResolution: 1.15→1.191 Å
RfactorNum. reflection
Rfree0.2052 -
Rwork0.2005 -
obs-7633

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