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- PDB-6p7a: CRYSTAL STRUCTURE OF THE FOWLPOX VIRUS HOLLIDAY JUNCTION RESOLVASE -

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Basic information

Entry
Database: PDB / ID: 6p7a
TitleCRYSTAL STRUCTURE OF THE FOWLPOX VIRUS HOLLIDAY JUNCTION RESOLVASE
ComponentsHolliday junction resolvase
KeywordsHYDROLASE / RESOLVASE
Function / homology
Function and homology information


crossover junction DNA endonuclease activity / hydrolase activity, acting on ester bonds / four-way junction DNA binding / DNA recombination / Hydrolases; Acting on ester bonds / DNA repair / magnesium ion binding
Similarity search - Function
Holliday junction resolvase, A22 / Poxvirus A22 protein / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
: / A22R orthologue / Holliday junction resolvase
Similarity search - Component
Biological speciesFowlpox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 3.081 Å
AuthorsLi, N. / Shi, K. / Banerjee, S. / Rao, T. / Aihara, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Sci Rep / Year: 2020
Title: Structural insights into the promiscuous DNA binding and broad substrate selectivity of fowlpox virus resolvase.
Authors: Li, N. / Shi, K. / Rao, T. / Banerjee, S. / Aihara, H.
History
DepositionJun 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 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

Downloads & links

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Assembly

Deposited unit
A: Holliday junction resolvase
B: Holliday junction resolvase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6998
Polymers34,0252
Non-polymers6746
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-52 kcal/mol
Surface area15390 Å2
MethodPISA
2
A: Holliday junction resolvase
hetero molecules

B: Holliday junction resolvase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6998
Polymers34,0252
Non-polymers6746
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z+1/31
Buried area2560 Å2
ΔGint-49 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.620, 82.620, 68.756
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Holliday junction resolvase


Mass: 17012.346 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fowlpox virus / Gene: FPV187 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A385H9X4, UniProt: Q9J546*PLUS
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION

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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: 3.98 Å3/Da / Density % sol: 69.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Trix/HCl, 10mM Cadmium hloride, 6% W/V PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.081→19.845 Å / Num. obs: 9345 / % possible obs: 96.3 % / Redundancy: 2.6 % / CC1/2: 1 / Rmerge(I) obs: 0.03 / Net I/σ(I): 13.1
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2480 / CC1/2: 0.8 / % possible all: 97.72

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Processing

Software
NameVersionClassification
PHENIX(dev_3512: ???)refinement
XDSdata reduction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 3.081→19.845 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 44.59
RfactorNum. reflection% reflection
Rfree0.279 437 4.68 %
Rwork0.2712 --
obs0.2716 9338 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.081→19.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 6 0 2343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022381
X-RAY DIFFRACTIONf_angle_d0.4863219
X-RAY DIFFRACTIONf_dihedral_angle_d2.8751432
X-RAY DIFFRACTIONf_chiral_restr0.044361
X-RAY DIFFRACTIONf_plane_restr0.004405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0812-3.52490.3639960.33213013X-RAY DIFFRACTION97
3.5249-4.43280.31041780.31162938X-RAY DIFFRACTION97
4.4328-19.84510.26281630.2462950X-RAY DIFFRACTION96
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)
15.5479-5.1823-4.93317.87975.44797.9622-1.0805-1.9758-0.21310.5891.695-1.2662-0.39932.07480.00351.06790.21810.50311.07660.23180.6397-16.626627.723521.2475
26.04740.0057-0.83399.2317-0.53347.1533-0.67220.6002-0.1782-0.02030.18350.27450.3759-0.79410.51451.12160.05080.46110.8698-0.02070.6627-8.743723.963310.4728
37.1487-8.4202-7.47919.93488.81227.82141.867-0.3083.1682-1.73070.3227-1.6657-2.46560.277-0.15592.57260.290.7590.8246-0.02881.1809-0.239233.500515.963
43.01161.5629-0.641.15450.16611.0953-0.3905-0.7458-1.83571.2195-0.1093-0.31521.7484-0.41062.08382.14310.58291.1051.05121.20041.4458-18.57715.776724.3486
58.2820.3675-2.5314.37720.28412.2592-0.3796-1.54110.1351.31960.0758-0.02791.13870.2745-0.65741.0751-0.08750.56140.93210.41820.3662-22.397821.59821.9574
67.37815.4177-4.92747.4255-1.89324.1837-1.57552.4476-0.2079-1.94691.29361.04440.3796-1.9536-0.4681.1259-0.3880.38240.992-0.22810.559616.733327.8052-3.4669
74.28460.3992-4.04635.4743-2.52618.6256-0.0941-0.83640.11670.8877-0.2778-0.1522-0.83930.68660.12231.214-0.12140.3420.9045-0.03150.61947.958325.68786.7256
85.8843-3.52121.44173.5645-1.33611.77440.4695-0.5509-1.4426-0.8235-0.23560.96570.9231-0.48154.97281.6942-0.79860.7590.8383-0.76121.219517.388714.3758-6.5078
92.0352-1.9655.32488.7709-2.46523.5683-0.24733.55230.6031-1.2231-0.1512-0.8630.76710.4148-0.721.23210.06510.50271.2978-0.39660.955522.183122.2233-5.1909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 78 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 117 )
5X-RAY DIFFRACTION5chain 'A' and (resid 118 through 147 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 34 )
7X-RAY DIFFRACTION7chain 'B' and (resid 35 through 84 )
8X-RAY DIFFRACTION8chain 'B' and (resid 85 through 115 )
9X-RAY DIFFRACTION9chain 'B' and (resid 116 through 148 )

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