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- PDB-4odg: Crystal structure of Staphylococcal nuclease variant V23I/V66I/V7... -

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Basic information

Entry
Database: PDB / ID: 4odg
TitleCrystal structure of Staphylococcal nuclease variant V23I/V66I/V74I/V99I at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / pdTp / cavity / pressure
Function / homology
Function and homology information


micrococcal nuclease / : / nucleic acid binding / extracellular region / metal ion binding / membrane
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
PHOSPHATE ION / THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsCaro, J.A. / Schlessman, J.L. / Heroux, A. / Garcia-Moreno E., B.
CitationJournal: To be Published
Title: Pressure effects in proteins
Authors: Caro, J.A. / Schlessman, J.L. / Garcia-Moreno E., B.
History
DepositionJan 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4374
Polymers16,8991
Non-polymers5373
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.786, 47.786, 63.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Thermonuclease / TNase / Micrococcal nuclease / Staphylococcal nuclease


Mass: 16899.436 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: V23I/V66I/V74I/V99I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: pET24a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00644, micrococcal nuclease
#2: Chemical ChemComp-THP / THYMIDINE-3',5'-DIPHOSPHATE


Type: DNA linking / Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 24% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2013
Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification
RadiationMonochromator: double crystal Si(111) with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. all: 14929 / Num. obs: 14929 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.062 / Χ2: 2.493 / Net I/σ(I): 19.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.73-1.769.50.21111.57541.0199.6
1.76-1.7910.70.187191.127100
1.79-1.8311.20.1717541.16499.7
1.83-1.8612.30.1627281.29299.9
1.86-1.9130.1497511.421100
1.9-1.9512.90.1157271.53799.9
1.95-212.30.1037561.77399.9
2-2.0513.10.0927411.827100
2.05-2.1112.70.0827432.078100
2.11-2.1812.50.087632.28100
2.18-2.26130.0757282.409100
2.26-2.3512.20.0727392.622100
2.35-2.4512.70.0697352.782100
2.45-2.5812.30.0657522.963100
2.58-2.7512.40.067493.212100
2.75-2.96120.067593.498100
2.96-3.2611.90.0567373.739100
3.26-3.7310.70.0557604.115100
3.73-4.6910.90.0597544.555100
4.69-509.80.0617804.78999.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.79 Å
Translation2.5 Å47.79 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SNC

1snc


Resolution: 1.73→47.79 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2546 / WRfactor Rwork: 0.2113 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8271 / SU B: 5.793 / SU ML: 0.099 / SU R Cruickshank DPI: 0.1185 / SU Rfree: 0.1222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 755 5.1 %RANDOM
Rwork0.1895 ---
all0.1918 14906 --
obs0.1918 14906 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.04 Å2 / Biso mean: 41.2144 Å2 / Biso min: 16.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2--1.02 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 1.73→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 31 61 1178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021147
X-RAY DIFFRACTIONr_angle_refined_deg1.9852.0111546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6985138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47824.68147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.79715228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.022155
X-RAY DIFFRACTIONr_chiral_restr0.1670.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021822
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 58 -
Rwork0.263 1028 -
all-1086 -
obs-1086 99.45 %
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)
13.23961.3429-0.21142.75-3.02866.9772-0.16820.26820.32840.42880.57680.0987-0.9663-0.7531-0.40860.22750.13130.00950.17730.01480.106423.276911.36580.6681
210.11713.46570.80056.9349-4.21046.6629-0.19110.01690.08711.08111.3760.8557-1.164-1.8016-1.18490.30180.39380.18280.57990.29330.229412.68537.98099.251
32.37241.6179-0.83023.9354-0.304116.25960.05510.0128-0.04280.3412-0.1859-0.3066-1.28770.67510.13070.2481-0.0324-0.07530.1088-0.05550.145831.66289.12114.5059
41.70410.2929-0.81752.202-3.04538.9742-0.04020.1852-0.06530.19020.2938-0.0483-0.2193-0.8506-0.25370.12090.0475-0.03580.1916-0.01450.116723.16323.51362.2918
53.82351.559-2.85173.5409-3.562511.0472-0.33840.1958-0.5118-0.41710.4514-0.22921.3935-1.2233-0.1130.251-0.1436-0.05130.1971-0.00780.158620.5527-6.59186.3325
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 46
2X-RAY DIFFRACTION2A47 - 66
3X-RAY DIFFRACTION3A67 - 78
4X-RAY DIFFRACTION4A79 - 113
5X-RAY DIFFRACTION5A114 - 141

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