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- PDB-4miu: Crystal structure of Staphylococcal nuclease variant Delta+PHS V2... -

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Basic information

Entry
Database: PDB / ID: 4miu
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS V23T/V99T at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant / pdtp / cavity / pressure
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 / molecular replacement / Resolution: 1.67 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
DepositionSep 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: 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

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Assembly

Deposited unit
A: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5903
Polymers16,1471
Non-polymers4422
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.204, 60.554, 38.201
Angle α, β, γ (deg.)90.000, 93.320, 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: Nuclease A (UNP residues 83-231) / Mutation: V23T, G50F,V51N,V99T,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-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.: 121 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 20% 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: 110 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jan 25, 2013 / Details: Multilayer
RadiationMonochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. all: 16555 / Num. obs: 16555 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.015 / Net I/σ(I): 46.5
Reflection shellResolution: 1.67→1.77 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 5.1 / Num. unique all: 2612 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.14 Å
Translation2.5 Å38.14 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
APEXdata collection
APEXdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BDC

3bdc


Resolution: 1.67→38.14 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2093 / WRfactor Rwork: 0.1646 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.818 / SU B: 2.379 / SU ML: 0.079 / SU R Cruickshank DPI: 0.1065 / SU Rfree: 0.1123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 835 5.1 %RANDOM
Rwork0.1841 ---
all0.1866 16528 --
obs0.1866 16528 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.96 Å2 / Biso mean: 24.0906 Å2 / Biso min: 11.46 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å20.26 Å2
2---1.13 Å20 Å2
3---2.25 Å2
Refinement stepCycle: LAST / Resolution: 1.67→38.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1033 0 26 121 1180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021153
X-RAY DIFFRACTIONr_angle_refined_deg1.90721571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0735152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93425.09851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62815232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.602155
X-RAY DIFFRACTIONr_chiral_restr0.1350.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021847
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 59 -
Rwork0.233 1133 -
all-1192 -
obs-1192 100 %

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