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- PDB-4oky: Crystal structure of PvuRts1I, a 5-hydroxymethylcytosine DNA rest... -

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Basic information

Entry
Database: PDB / ID: 4oky
TitleCrystal structure of PvuRts1I, a 5-hydroxymethylcytosine DNA restriction endonuclease
ComponentsRestriction endonuclease PvuRts1 I
KeywordsDNA BINDING PROTEIN / SRA-like domain / restriction endonuclease
Function / homologySET and RING associated domain / : / SET and RING associated domain / Restriction endonuclease PvuRts1 I-like, N-terminal / endonuclease activity / Restriction endonuclease PvuRts1 I
Function and homology information
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsWang, C.L. / Shao, C. / Zang, J.Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural basis for the substrate selectivity of PvuRts1I, a 5-hydroxymethylcytosine DNA restriction endonuclease
Authors: Shao, C. / Wang, C. / Zang, J.
History
DepositionJan 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Restriction endonuclease PvuRts1 I


Theoretical massNumber of molelcules
Total (without water)34,5241
Polymers34,5241
Non-polymers00
Water00
1
C: Restriction endonuclease PvuRts1 I

C: Restriction endonuclease PvuRts1 I


Theoretical massNumber of molelcules
Total (without water)69,0482
Polymers69,0482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area1620 Å2
ΔGint-11 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.210, 160.210, 45.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Restriction endonuclease PvuRts1 I / Restriction endonuclease PvuRts1I


Mass: 34524.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: pvuRts1I / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q52612
Has protein modificationY

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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: 4.19 Å3/Da / Density % sol: 70.67 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 1.128M NaH2PO4, 0.752M K2HPO4, 0.1M CAPS pH 10.5, 0.19M Li2SO4, 6%(v/v) glycerol , VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 25, 2013
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.9→56.71 Å / Num. all: 13568 / Num. obs: 13311 / % possible obs: 98.1 % / Observed criterion σ(F): 12.9 / Observed criterion σ(I): 12.9 / Redundancy: 10.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→56.71 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.876 / SU B: 14.504 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R: 0.562 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28695 662 5 %RANDOM
Rwork0.25202 ---
obs0.25373 12620 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.258 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0 Å20 Å2
2---0.95 Å2-0 Å2
3---1.9 Å2
Refinement stepCycle: LAST / Resolution: 2.9→56.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 0 0 0 2184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192229
X-RAY DIFFRACTIONr_bond_other_d0.0050.022023
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9413031
X-RAY DIFFRACTIONr_angle_other_deg0.84734592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4845280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11123.645107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.47815330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1531516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022588
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02548
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1545.8271129
X-RAY DIFFRACTIONr_mcbond_other3.1535.8231128
X-RAY DIFFRACTIONr_mcangle_it5.2648.7231406
X-RAY DIFFRACTIONr_mcangle_other3.9468.3031407
X-RAY DIFFRACTIONr_scbond_it2.9975.8141100
X-RAY DIFFRACTIONr_scbond_other4.065.4611076
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1358.131592
X-RAY DIFFRACTIONr_long_range_B_refined5.47343.6152552
X-RAY DIFFRACTIONr_long_range_B_other5.47443.5882550
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 46 -
Rwork0.322 932 -
obs--98.39 %

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