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- PDB-5e6f: Canarypox virus resolvase -

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Basic information

Entry
Database: PDB / ID: 5e6f
TitleCanarypox virus resolvase
ComponentsCNPV261 Holliday junction resolvase protein
KeywordsVIRAL PROTEIN / Poxvirus / Resolvase / Holliday Junction / Metal-binding
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / four-way junction DNA binding / DNA recombination / DNA repair / magnesium ion binding
Similarity search - Function
Holliday junction resolvase, A22 / Poxvirus A22 protein / Ribonuclease H-like superfamily
Similarity search - Domain/homology
D(-)-TARTARIC ACID / CNPV261 Holliday junction resolvase protein
Similarity search - Component
Biological speciesCanarypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsLi, H. / Hwang, Y. / Perry, K. / Bushman, F.D. / Van Duyne, G.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI057168 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U01 AI 082015 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structure and Metal Binding Properties of a Poxvirus Resolvase.
Authors: Li, H. / Hwang, Y. / Perry, K. / Bushman, F. / Van Duyne, G.D.
History
DepositionOct 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2May 4, 2016Group: Data collection / Structure summary
Revision 1.3Jun 8, 2016Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CNPV261 Holliday junction resolvase protein
B: CNPV261 Holliday junction resolvase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3635
Polymers35,1642
Non-polymers1993
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-29 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.117, 89.117, 117.945
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CNPV261 Holliday junction resolvase protein


Mass: 17581.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canarypox virus / Gene: CNPV261 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6VZ86
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.35 Å3/Da / Density % sol: 65 % / Description: long pyramid
Crystal growTemperature: 295 K / Method: microdialysis / pH: 8.5
Details: Crystals generally appeared after one week and continued to grow for another week to typical dimensions of 0.1 x 0.1 x 0.5 mm
PH range: 8.0 - 8.5 / Temp details: 295K incubator

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.42→89.12 Å / Num. obs: 18653 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.042 / Net I/σ(I): 14.5 / Num. measured all: 117127
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.42-2.516.41.9171.41231319150.6110.80499.9
9.05-89.125.10.02548.920223970.9990.01294.7

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Processing

Software
NameVersionClassification
CNSrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0073refinement
RefinementMethod to determine structure: SAD
Starting model: 1KCF

1kcf


Resolution: 2.6→50 Å / FOM work R set: 0.8289 / Cross valid method: THROUGHOUT / σ(F): 1363
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 624 4.1 %RANDOM
Rwork0.2234 12057 --
obs-12681 83.3 %-
Solvent computationBsol: 51.0483 Å2
Displacement parametersBiso max: 113.66 Å2 / Biso mean: 65.88 Å2 / Biso min: 38.88 Å2
Baniso -1Baniso -2Baniso -3
1-11.845 Å20 Å20 Å2
2--11.845 Å20 Å2
3----23.689 Å2
Refinement stepCycle: final / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2112 0 12 35 2159
Biso mean--94.57 52.88 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_scbond_it1.8212
X-RAY DIFFRACTIONc_mcangle_it2.4112
X-RAY DIFFRACTIONc_scangle_it2.8792.5
LS refinement shellResolution: 2.6→2.72 Å / Rfactor Rfree: 0.3084 / Rfactor Rwork: 0.2988
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6tar_xplor_par.txt

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