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- PDB-5h4h: Structure of PIN-domain protein (VapC4 toxin) from Pyrococcus hor... -

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Basic information

Entry
Database: PDB / ID: 5h4h
TitleStructure of PIN-domain protein (VapC4 toxin) from Pyrococcus horikoshii determined at 2.2 A resolution
ComponentsRibonuclease VapC4
KeywordsHYDROLASE / Pyrococcus horikoshii / hypothetical protein / PIN-domain
Function / homology
Function and homology information


RNA nuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding
Similarity search - Function
Probable ribonuclease VapC, Thermococci / VapC family / 5'-nuclease / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Ribonuclease VapC4
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsBiswas, A. / Hatti, K. / Srinivasan, N. / Murthy, M.R.N. / Sekar, K.
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Structure determination of contaminant proteins using the MarathonMR procedure
Authors: Hatti, K. / Biswas, A. / Chaudhary, S. / Dadireddy, V. / Sekar, K. / Srinivasan, N. / Murthy, M.R.N.
History
DepositionOct 31, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Ribonuclease VapC4
B: Ribonuclease VapC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6454
Polymers34,4212
Non-polymers2252
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-32 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.970, 45.260, 53.620
Angle α, β, γ (deg.)90.00, 104.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease VapC4 / PIN-domain protein


Mass: 17210.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Strain: OT3 / Gene: vapC4, PH0500 / Production host: Escherichia coli (E. coli)
References: UniProt: O58236, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 1.77 Å3/Da / Density % sol: 30.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Sodium acetate trihydrate, 0.1M Tris-HCl, 30%(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.54179 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.21→51.85 Å / Num. obs: 11886 / % possible obs: 97.2 % / Redundancy: 3.3 % / Net I/σ(I): 8.5
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.54 / % possible all: 71.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V96

1v96


Resolution: 2.23→51.85 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9 / SU B: 9.757 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.514 / ESU R Free: 0.268 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25904 661 5.6 %RANDOM
Rwork0.20707 ---
obs0.21012 11212 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.159 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å2-0.76 Å2
2--0.94 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: 1 / Resolution: 2.23→51.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 2 19 2306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022332
X-RAY DIFFRACTIONr_bond_other_d0.0010.022341
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9993174
X-RAY DIFFRACTIONr_angle_other_deg0.90935394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6155291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50225.38591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77315435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.927159
X-RAY DIFFRACTIONr_chiral_restr0.0660.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212524
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
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_it1.0442.781158
X-RAY DIFFRACTIONr_mcbond_other1.0412.7781157
X-RAY DIFFRACTIONr_mcangle_it1.7774.161445
X-RAY DIFFRACTIONr_mcangle_other1.7764.1621446
X-RAY DIFFRACTIONr_scbond_it1.1342.9361174
X-RAY DIFFRACTIONr_scbond_other1.1332.9381175
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9424.3351728
X-RAY DIFFRACTIONr_long_range_B_refined3.0933.0962590
X-RAY DIFFRACTIONr_long_range_B_other3.08833.1082590
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.232→2.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 41 -
Rwork0.259 797 -
obs--97.33 %

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