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- PDB-2oeo: Cryogenic crystal structure of Staphylococcal Nuclease variant tr... -

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Basic information

Entry
Database: PDB / ID: 2oeo
TitleCryogenic crystal structure of Staphylococcal Nuclease variant truncated Delta+PHS I92D
ComponentsStaphylococcal thermonuclease
KeywordsHYDROLASE / OB-fold
Function / homology
Function and homology information


micrococcal nuclease / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / nucleic acid binding / extracellular region / membrane / metal ion binding
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsReynald, R.L. / Lattman, E.E. / Gittis, A.G.
CitationJournal: To be Published
Title: Buried Charges and Water in the Protein Interior: Reality or Fiction?
Authors: Reynald, R.L. / Gitti, R.K. / Lattman, E.E. / Gittis, A.G.
History
DepositionDec 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_conn / 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_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.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 / _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

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Assembly

Deposited unit
A: Staphylococcal thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8553
Polymers15,4121
Non-polymers4422
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.452, 57.630, 34.618
Angle α, β, γ (deg.)90.00, 99.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Staphylococcal thermonuclease / E.C.3.1.31.1 / TNase / Micrococcal nuclease / Staphylococcal nuclease


Mass: 15412.453 Da / Num. of mol.: 1 / Mutation: G50F, V51N, I92D, P117G, H124L, S128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: FOGGI / Gene: nuc / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21 / References: UniProt: P00644, micrococcal nuclease
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-THP / THYMIDINE-3',5'-DIPHOSPHATE


Type: DNA linking / Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 1.94 Å3/Da / Density % sol: 36.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20-35% MPD, 10% glycerol, 5% DMSO, 10.5 mM potassium phosphate in the presence of Ca2+ and pdTp, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 24, 2001 / Details: mirrors (Osmic)
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20.79 Å / Num. all: 8029 / Num. obs: 8029 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 8.1 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.13 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1212 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
CNS1.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SNC

1snc


Resolution: 2→20.79 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 793452.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 673 8.4 %RANDOM
Rwork0.196 ---
all0.1961 ---
obs0.1961 8029 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.208 Å2 / ksol: 0.376369 e/Å3
Displacement parametersBiso mean: 10.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å22.38 Å2
2---0.46 Å20 Å2
3---1.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-6 Å
Luzzati sigma a0.16 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2→20.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1019 0 26 59 1104
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_mcbond_it1.071.5
X-RAY DIFFRACTIONc_mcangle_it1.472
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 97 7.4 %
Rwork0.206 1212 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3thp_xplor_par.txtthp_xplor_top.txt
X-RAY DIFFRACTION4ion.paramion.top

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