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- PDB-3mvv: Crystal structure of Staphylococcal nuclease variant Delta+PHS F3... -

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Basic information

Entry
Database: PDB / ID: 3mvv
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS F34A at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant / pdtp / pressure / cavity
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 / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsCaro, J.A. / Schlessman, J.L. / Garcia-Moreno, E.B. / Heroux, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Cavities determine the pressure unfolding of proteins.
Authors: Roche, J. / Caro, J.A. / Norberto, D.R. / Barthe, P. / Roumestand, C. / Schlessman, J.L. / Garcia, A.E. / Garcia-Moreno E, B. / Royer, C.A.
History
DepositionMay 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 6, 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)16,5103
Polymers16,0671
Non-polymers4422
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.577, 61.163, 38.620
Angle α, β, γ (deg.)90.00, 92.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16067.365 Da / Num. of mol.: 1 / Fragment: Deletion UNP residues 126-131 / Mutation: F34A,G132F,V133N,P199G,S210A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pET24a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00644, UniProt: Q8NXI6*PLUS, 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.: 79 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 25% 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: 1.008 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. all: 15190 / Num. obs: 15190 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.058 / Χ2: 1.969 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.72-1.756.90.287330.946199.9
1.75-1.787.30.227660.998199.9
1.78-1.827.30.2017511.035199.7
1.82-1.857.40.1727751.0851100
1.85-1.897.40.1547371.1731100
1.89-1.947.40.137871.3341100
1.94-1.997.50.1197141.3511100
1.99-2.047.40.17981.5861100
2.04-2.17.40.0947361.714199.9
2.1-2.177.40.0847701.7831100
2.17-2.247.40.0797371.998199.5
2.24-2.337.40.0747732.053199.7
2.33-2.447.40.077482.2591100
2.44-2.577.40.0647802.306199.9
2.57-2.737.40.0647522.6311100
2.73-2.947.30.0617592.951100
2.94-3.247.10.0567733.296199.9
3.24-3.7170.0457593.2791100
3.71-4.6770.0427673.006199.4
4.67-506.90.047752.706196.9

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Phasing

Phasing MRRfactor: 39.81 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.58 Å
Translation2.5 Å38.58 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BDC with all H2O, Ca2+ and THP removed and the following truncations: H8A, T13A, Q30A, F34A, K64A, T82A, Y113A, V114A, Y115A; all b-factors were reset to 20.

3bdc


Resolution: 1.72→38.58 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.191 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.851 / SU B: 2.252 / SU ML: 0.075 / SU R Cruickshank DPI: 0.123 / SU Rfree: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1516 10 %RANDOM
Rwork0.182 ---
all0.1824 15167 --
obs0.187 15120 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.09 Å2 / Biso mean: 22.533 Å2 / Biso min: 10.85 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20.75 Å2
2---1.06 Å20 Å2
3---3.05 Å2
Refinement stepCycle: LAST / Resolution: 1.72→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1027 0 26 79 1132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221187
X-RAY DIFFRACTIONr_angle_refined_deg1.5812.0041614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2385153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.0742548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.6215237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.289155
X-RAY DIFFRACTIONr_chiral_restr0.1370.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021872
X-RAY DIFFRACTIONr_mcbond_it1.5431.5709
X-RAY DIFFRACTIONr_mcangle_it2.39921152
X-RAY DIFFRACTIONr_scbond_it3.6343478
X-RAY DIFFRACTIONr_scangle_it5.6744.5457
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 118 -
Rwork0.239 991 -
all-1109 -
obs--99.37 %

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