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- PDB-4rkb: Crystal structure of Staphylococcal nuclease variant Delta+PHS V6... -

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Basic information

Entry
Database: PDB / ID: 4rkb
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS V66T/V99T 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: 1.88 Å
AuthorsCaro, J.A. / Schlessman, J.L. / Garcia-Moreno E., B.
CitationJournal: to be published
Title: Cavities in proteins
Authors: Caro, J.A. / Schlessman, J.L. / Garcia-Moreno E., B.
History
DepositionOct 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Sep 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

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Assembly

Deposited unit
A: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5903
Polymers16,1471
Non-polymers4422
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.975, 60.544, 37.948
Angle α, β, γ (deg.)90.000, 93.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thermonuclease


Mass: 16147.408 Da / Num. of mol.: 1 / Fragment: UNP residues 83-232
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 30% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp , pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jan 23, 2014 / Details: Multilayer
RadiationMonochromator: GE111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.88→60.54 Å / Num. all: 11479 / Num. obs: 11479 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.64 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 26.46
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID% possible all
2.09-2.157.580.1984.176691100
2.15-2.217.990.1626221100
2.21-2.288.320.1596481100
2.28-2.369.010.1336341100
2.36-2.459.380.1186151100
2.45-2.5510.20.1016091100
2.55-2.6710.830.085961100
2.67-2.8112.040.0845791100
2.81-2.9913.30.0615961100
2.99-3.2316.50.0555941100
3.23-3.5619.050.0485811100
3.56-4.119.760.0415831100
4.1-5.1821.030.0385821100
5.18-60.5424.950.042575199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.12 Å
Translation2.5 Å32.12 Å

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Processing

Software
NameVersionClassificationNB
XPREP2008/2 for Windowsdata reduction
PHASER2.3.0phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
APEXdata collection
APEXdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BDC

3bdc


Resolution: 1.88→37.89 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2154 / WRfactor Rwork: 0.1793 / FOM work R set: 0.8345 / SU B: 3.39 / SU ML: 0.1 / SU R Cruickshank DPI: 0.1512 / SU Rfree: 0.1398 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 548 4.8 %RANDOM
Rwork0.1854 ---
all0.1874 11462 --
obs0.1874 11462 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.56 Å2 / Biso mean: 27.027 Å2 / Biso min: 12.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20.29 Å2
2---0.43 Å20 Å2
3---1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.88→37.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1033 0 26 65 1124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021109
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.9991502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92324.89849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22315215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.328155
X-RAY DIFFRACTIONr_chiral_restr0.140.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021811
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 34 -
Rwork0.229 787 -
all-821 -
obs-821 100 %

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