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- PDB-1ynm: Crystal structure of restriction endonuclease HinP1I -

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Basic information

Entry
Database: PDB / ID: 1ynm
TitleCrystal structure of restriction endonuclease HinP1I
ComponentsR.HinP1I restriction endonuclease
KeywordsHYDROLASE / Restriction endonuclease / dimerizaton
Function / homologyTrna Endonuclease; Chain: A, domain 1 - #40 / Restriction endonuclease, type II, HinP1I / R.HinP1I restriction endonuclease / Trna Endonuclease; Chain: A, domain 1 / endonuclease activity / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / R.HinP1I restriction endonuclease
Function and homology information
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.65 Å
AuthorsYang, Z. / Horton, J.R. / Maunus, R. / Wilson, G.G. / Roberts, R.J. / Cheng, X.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI
Authors: Yang, Z. / Horton, J.R. / Maunus, R. / Wilson, G.G. / Roberts, R.J. / Cheng, X.
History
DepositionJan 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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

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Assembly

Deposited unit
A: R.HinP1I restriction endonuclease


Theoretical massNumber of molelcules
Total (without water)28,7921
Polymers28,7921
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.218, 117.218, 114.472
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsThe asymmetric unit of the crystal structure contain one biological unit.

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Components

#1: Protein R.HinP1I restriction endonuclease


Mass: 28791.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: hinP1IR / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): PR1
References: UniProt: Q5I6E6, type II site-specific deoxyribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 4.2 Å3/Da / Density % sol: 70.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, sodium chloride, ammonium acetate, MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 27, 1998
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.6→22 Å / Num. all: 14790 / Num. obs: 14790 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.9 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 5.1 / Num. unique all: 714 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.65→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1541322.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 693 5 %RANDOM
Rwork0.221 ---
obs0.221 13977 99.9 %-
all-13977 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.7455 Å2 / ksol: 0.339586 e/Å3
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.13 Å25.75 Å20 Å2
2---4.13 Å20 Å2
3---8.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 0 100 2082
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.65→2.74 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.421 83 5.6 %
Rwork0.339 2142 -
obs-1367 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION4WATER_REP.PARAM
X-RAY DIFFRACTION5ION.PARAM

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