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- PDB-4o88: Crystal structure of a C-tagged Nuclease -

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Basic information

Entry
Database: PDB / ID: 4o88
TitleCrystal structure of a C-tagged Nuclease
ComponentsN-tagged Nuclease
KeywordsHYDROLASE / Novel fold / Nuclease
Function / homologyUncharacterized protein
Function and homology information
Biological speciesMillerozyma acaciae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molecular refinement / Resolution: 2.9 Å
AuthorsChakravarty, A.K. / Smith, P. / Shuman, S.
CitationJournal: Cell Rep / Year: 2014
Title: Structure, mechanism, and specificity of a eukaryal tRNA restriction enzyme involved in self-nonself discrimination.
Authors: Chakravarty, A.K. / Smith, P. / Jalan, R. / Shuman, S.
History
DepositionDec 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-tagged Nuclease
B: N-tagged Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,99323
Polymers74,0972
Non-polymers1,89621
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: N-tagged Nuclease
B: N-tagged Nuclease
hetero molecules

A: N-tagged Nuclease
B: N-tagged Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,98746
Polymers148,1944
Non-polymers3,79242
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3920 Å2
ΔGint-189 kcal/mol
Surface area31290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.879, 77.455, 147.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein N-tagged Nuclease


Mass: 37048.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Millerozyma acaciae (fungus) / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / References: UniProt: Q707V3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100 mM Sodium citrate, 3 - 3.5 M Ammonium sulfate, 100 mM Magnesium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.176 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.176 Å / Relative weight: 1
ReflectionResolution: 2.9→45.95 Å / Num. all: 16413 / Num. obs: 16216 / % possible obs: 98.8 % / Observed criterion σ(F): 9999 / Observed criterion σ(I): 9999
Reflection shellResolution: 2.9→3.07 Å / % possible all: 94.4

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
Aimlessdata scaling
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: Molecular refinement / Resolution: 2.9→45.95 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 24.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 610 3.78 %
Rwork0.1879 --
obs0.1901 16139 98.52 %
all-16413 -
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4975 0 97 164 5236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055135
X-RAY DIFFRACTIONf_angle_d1.0656940
X-RAY DIFFRACTIONf_dihedral_angle_d16.4171892
X-RAY DIFFRACTIONf_chiral_restr0.046777
X-RAY DIFFRACTIONf_plane_restr0.003884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.19190.32751460.24343699X-RAY DIFFRACTION96
3.1919-3.65360.27261530.20143878X-RAY DIFFRACTION99
3.6536-4.60250.22371530.15733883X-RAY DIFFRACTION99
4.6025-45.95870.2121580.18254069X-RAY DIFFRACTION99
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)
12.38560.5513-0.75360.1365-0.43581.0088-0.11210.15340.02640.0750.0289-0.05680.02740.0164-00.29430.0479-0.02490.1541-0.05910.29031.164337.388772.318
22.7110.57-0.5670.184-0.07911.78120.116-0.0688-0.1270.19850.0163-0.0630.1110.013500.30770.00420.00540.15480.00980.3177-1.435841.228378.8166
31.37581.136-0.95451.6705-0.07131.26870.0658-0.043-0.0179-0.0849-0.06950.06950.0238-0.135-00.3016-0.0116-0.02330.24010.00260.3526-27.453732.501987.0548
41.20780.31830.01861.7973-0.30391.02280.0324-0.477-0.6719-0.1099-0.1136-0.45820.34240.6314-0.00230.51840.009-0.00720.5943-0.020.60594.590546.863284.8106
53.1861-0.4279-0.90690.5390.27390.9693-0.01680.1273-0.1455-0.0405-0.00310.07440.005-0.179300.3158-0.03670.00250.28360.01350.2506-0.875634.9161124.5705
63.233-0.289-1.11670.5535-0.37722.75590.18310.6532-0.1347-0.2043-0.1155-0.01040.1573-0.0966-0.00010.366-0.0088-0.00420.4468-0.05190.28861.684139.3709118.5568
73.1112-0.7528-1.4332.05430.72154.24450.04410.13870.0553-0.08380.02010.09770.2416-0.19640.00010.4076-0.03520.03480.5040.02080.295923.11734.6581109.1691
80.89690.55710.3380.73140.76670.9720.26371.4702-0.25780.0429-0.04450.2637-0.187-0.8842-0.00150.57990.15150.0840.9980.14320.6519-11.249544.1405114.6922
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 103 )
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 197 )
3X-RAY DIFFRACTION3chain 'A' and (resid 198 through 261 )
4X-RAY DIFFRACTION4chain 'A' and (resid 262 through 318 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 103 )
6X-RAY DIFFRACTION6chain 'B' and (resid 104 through 198 )
7X-RAY DIFFRACTION7chain 'B' and (resid 199 through 282 )
8X-RAY DIFFRACTION8chain 'B' and (resid 283 through 318 )

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