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- PDB-8fr5: Crystal structure of the Human Smacovirus 1 Rep domain -

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Basic information

Entry
Database: PDB / ID: 8fr5
TitleCrystal structure of the Human Smacovirus 1 Rep domain
ComponentsRep
KeywordsREPLICATION / DNA binding protein / endonuclease / viral protein
Function / homology: / Rep
Function and homology information
Biological speciesHuman smacovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsLimon, L.K. / Shi, K. / Dao, A. / Rugloski, J. / Tompkins, K.J. / Aihara, H. / Gordon, W.R. / Evans IIII, R.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM119483 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: The crystal structure of the human smacovirus 1 Rep domain.
Authors: Limon, L.K. / Shi, K. / Dao, A. / Rugloski, J. / Tompkins, K.J. / Aihara, H. / Gordon, W.R. / Evans 3rd, R.L.
History
DepositionJan 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rep
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6354
Polymers11,5341
Non-polymers1013
Water81145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.160, 49.370, 31.380
Angle α, β, γ (deg.)90.000, 110.301, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Rep


Mass: 11533.931 Da / Num. of mol.: 1 / Mutation: Y81F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human smacovirus 1 / Strain: France/2/2008/2548 / Gene: Rep / Plasmid: pTD68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B5CMT4
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.96 Å3/Da / Density % sol: 37.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Sodium Acetate pH 5.0, 20% PEG 4000, 1 M Guanidine HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.33→29.43 Å / Num. obs: 19703 / % possible obs: 95.46 % / Redundancy: 3.6 % / Biso Wilson estimate: 20.79 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.04161 / Rpim(I) all: 0.02461 / Rrim(I) all: 0.04858 / Net I/σ(I): 14.08
Reflection shellResolution: 1.33→1.378 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.8219 / Mean I/σ(I) obs: 2.51 / Num. unique obs: 5923 / CC1/2: 0.757 / CC star: 0.928 / Rpim(I) all: 0.5037 / Rrim(I) all: 0.9694 / % possible all: 82.91

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→29.43 Å / SU ML: 0.1788 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.8462
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2241 3643 9.91 %
Rwork0.1871 33122 -
obs0.1909 19613 91.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.77 Å2
Refinement stepCycle: LAST / Resolution: 1.33→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms736 0 3 45 784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045757
X-RAY DIFFRACTIONf_angle_d0.76761030
X-RAY DIFFRACTIONf_chiral_restr0.0794108
X-RAY DIFFRACTIONf_plane_restr0.006131
X-RAY DIFFRACTIONf_dihedral_angle_d18.9506100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.350.4743890.4485858X-RAY DIFFRACTION62.14
1.35-1.370.4271440.35851213X-RAY DIFFRACTION87.49
1.37-1.390.36061300.31651202X-RAY DIFFRACTION86.89
1.39-1.410.31541290.29941245X-RAY DIFFRACTION88.42
1.41-1.430.2751470.26951274X-RAY DIFFRACTION88.98
1.43-1.450.29691290.25971196X-RAY DIFFRACTION88.93
1.45-1.480.2841390.23251273X-RAY DIFFRACTION90.69
1.48-1.50.32411380.23861287X-RAY DIFFRACTION90.36
1.5-1.530.30961320.23951224X-RAY DIFFRACTION90.22
1.53-1.560.271390.22661264X-RAY DIFFRACTION88.69
1.56-1.60.2791410.1971261X-RAY DIFFRACTION91.1
1.6-1.630.23491520.1831329X-RAY DIFFRACTION94.88
1.63-1.680.2431440.17791303X-RAY DIFFRACTION95.07
1.68-1.720.22441490.181350X-RAY DIFFRACTION94.81
1.72-1.770.21341510.1791318X-RAY DIFFRACTION94.71
1.77-1.830.25751470.16941352X-RAY DIFFRACTION95.24
1.83-1.890.18451430.17741313X-RAY DIFFRACTION95.85
1.89-1.970.27411490.17591334X-RAY DIFFRACTION95
1.97-2.060.23231310.16761318X-RAY DIFFRACTION93.97
2.06-2.170.16121390.17581285X-RAY DIFFRACTION92.95
2.17-2.30.22161500.17531290X-RAY DIFFRACTION93.32
2.3-2.480.23171500.19981327X-RAY DIFFRACTION94.98
2.48-2.730.19521500.19311338X-RAY DIFFRACTION95.32
2.73-3.130.23551440.19621338X-RAY DIFFRACTION94.82
3.13-3.940.21091420.17811329X-RAY DIFFRACTION94.54
3.94-29.430.20871450.16921301X-RAY DIFFRACTION93.9

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