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- PDB-3v2t: Crystal structure of Staphylococcal nuclease variant Delta+PHS I9... -

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Basic information

Entry
Database: PDB / ID: 3v2t
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS I92A/V66A at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant / 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
THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsCaro, J.A. / Schlessman, J.L. / 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
DepositionDec 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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)16,5163
Polymers16,0731
Non-polymers4422
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.112, 60.382, 38.473
Angle α, β, γ (deg.)90.00, 94.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16073.328 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: G50F,V51N,V66A,I92A,P117G,H124L,S128A,del(44-49)
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-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.: 115 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jan 25, 2011 / Details: Multi-layer optics
RadiationMonochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25.047 Å / Num. all: 13233 / Num. obs: 13205 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.022 / Net I/σ(I): 33.6
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 4.97 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 6.09 / Num. unique all: 1805 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å25.05 Å
Translation2.5 Å25.05 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.2.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
APEXdata collection
APEXdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BDC

3bdc


Resolution: 1.8→25.047 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2134 / WRfactor Rwork: 0.1607 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8535 / SU B: 5.089 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1244 / SU Rfree: 0.1307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 1306 9.9 %RANDOM
Rwork0.1614 ---
all0.167 13205 --
obs0.167 13205 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.33 Å2 / Biso mean: 21.1204 Å2 / Biso min: 7.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20.55 Å2
2---1.19 Å20 Å2
3---2.12 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1028 0 26 115 1169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221117
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.9981513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6042550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76315218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.65155
X-RAY DIFFRACTIONr_chiral_restr0.1270.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021819
X-RAY DIFFRACTIONr_mcbond_it1.2311.5659
X-RAY DIFFRACTIONr_mcangle_it1.82921059
X-RAY DIFFRACTIONr_scbond_it3.1713458
X-RAY DIFFRACTIONr_scangle_it4.6734.5447
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 96 -
Rwork0.175 893 -
all-989 -
obs--100 %
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)
12.20080.0293-0.01713.54590.84891.0485-0.0572-0.0489-0.27590.12820.05170.00230.08950.06250.00540.08350.0290.00080.05090.01370.061213.18420.81853.5698
21.8303-3.8225-0.22736.7581.09580.08220.14930.0793-0.0907-0.3909-0.092-0.3329-0.0925-0.0007-0.05730.07530.01680.01810.0662-0.00970.084317.79881.01970.0583
32.7057-0.33430.10982.99760.58981.3722-0.0984-0.2704-0.04740.34780.0490.03650.09390.07290.04940.12080.0103-0.00350.12710.01940.054910.32298.19578.4993
42.6888-0.9114-0.12362.23760.45030.2608-0.03970.03670.04280.00240.01450.17760.0213-0.01560.02520.052-0.0059-0.00130.06140.00780.05036.054212.58572.1262
511.63192.92165.14997.42-1.12119.892-0.2934-0.91661.01090.84440.03180.4007-0.2653-0.2360.26160.12320.08790.06910.113-0.13120.05160.106121.099915.3986
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 27
2X-RAY DIFFRACTION2A28 - 35
3X-RAY DIFFRACTION3A36 - 80
4X-RAY DIFFRACTION4A81 - 131
5X-RAY DIFFRACTION5A132 - 141

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