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- PDB-9pqf: Xray crystal structure of Vientovirus FB Rep endonuclease domain ... -

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Basic information

Entry
Database: PDB / ID: 9pqf
TitleXray crystal structure of Vientovirus FB Rep endonuclease domain 2-114 with Mg2+ ion
ComponentsReplication-associated protein
KeywordsREPLICATION / Endonuclease / DNA binding protein / Viral protein
Function / homology
Function and homology information


nucleotidyltransferase activity / endonuclease activity / DNA replication / RNA helicase activity / hydrolase activity / host cell nucleus / DNA binding / RNA binding / ATP binding / metal ion binding
Similarity search - Function
: / CRESS-DNA virus replication initiator protein (Rep) endonuclease domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MALONATE ION / Replication-associated protein
Similarity search - Component
Biological speciesHuman lung-associated vientovirus FB
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMontermoso, S. / Gupta, K. / Pumroy, R.A. / Moiseenkova-Bell, V. / Bushman, F.D. / Van Duyne, G.D.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P30AI045008 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM108751 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI007632 United States
Department of Health & Human Services (HHS)S10OD018483 United States
National Science Foundation (NSF, United States)DMR2342336 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1P30GM124166 United States
CitationJournal: To Be Published
Title: Structures of nucleotide-bound Redondovirus Rep protein link conformation and function
Authors: Montermoso, S. / Gupta, K. / Pumroy, R.A. / Moiseenkova-Bell, V. / Bushman, F.D. / Van Duyne, G.D.
History
DepositionJul 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replication-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0303
Polymers12,9041
Non-polymers1262
Water88349
1
A: Replication-associated protein
hetero molecules

A: Replication-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0606
Polymers25,8082
Non-polymers2534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area2390 Å2
ΔGint-25 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.944, 62.974, 64.705
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-332-

HOH

31A-347-

HOH

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Components

#1: Protein Replication-associated protein / ATP-dependent helicase Rep / RepP


Mass: 12903.830 Da / Num. of mol.: 1 / Mutation: T2S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human lung-associated vientovirus FB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4D6K5Y8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 100 mM ammonium malonate pH 5.8, 200 mM potassium fluoride, 15% w/v PEG 4000, 15% v/v ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 27, 2024 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.8→45.13 Å / Num. obs: 9971 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 23.34 Å2 / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.076 / Rrim(I) all: 0.209 / Net I/σ(I): 5.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 1 / Num. unique obs: 475 / CC1/2: 0.816 / Rpim(I) all: 0.171 / Rrim(I) all: 0.466

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Processing

Software
NameVersionClassification
PHENIX1.21-5207refinement
DIALSdev20231129data scaling
DIALSdev20231129data reduction
PHASER2.8.3phasing
PDB_EXTRACT4.3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.13 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 982 9.85 %Random selection
Rwork0.1799 ---
obs0.1836 9970 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.91 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 8 49 961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007922
X-RAY DIFFRACTIONf_angle_d0.91246
X-RAY DIFFRACTIONf_dihedral_angle_d13.949348
X-RAY DIFFRACTIONf_chiral_restr0.061147
X-RAY DIFFRACTIONf_plane_restr0.006160
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork
1.8-1.890.29215911.40.2461237
1.89-2.010.2786153110.19971239
2.01-2.170.25271369.60.19011275
2.17-2.390.24381309.20.17971281
2.39-2.730.21231067.50.1871311
2.73-3.440.20981409.70.18491296
3.44-45.130.186215810.50.16051349

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