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- PDB-3r3o: Crystal structure of Staphylococcal nuclease variant Delta+PHS T6... -

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Basic information

Entry
Database: PDB / ID: 3r3o
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS T62A at cryogenic temperature and with high redundancy
ComponentsThermonuclease
KeywordsHYDROLASE / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsCaro, J.A. / Schlessman, J.L. / Garcia-Moreno E., B.
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
DepositionMar 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Sep 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

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Assembly

Deposited unit
A: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5563
Polymers16,1131
Non-polymers4422
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.132, 60.612, 37.632
Angle α, β, γ (deg.)90.00, 94.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16113.438 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231)
Mutation: UNP G132F,V133N,T144A,P199G,H206L,S210A,del(126-131)
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, UniProt: Q8NXI6*PLUS, 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.: 96 / 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: 44.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 21% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 8.0, 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
DetectorType: APEX II CCD / Detector: CCD / Date: Jan 25, 2010 / Details: multilayer
RadiationMonochromator: GE111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 11069 / Num. obs: 11067 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.42 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.0333 / Net I/σ(I): 22.76
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.2658 / Mean I/σ(I) obs: 3.34 / Num. unique all: 347 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å31.91 Å
Translation2.5 Å31.91 Å

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
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: 1.9→31.91 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2127 / WRfactor Rwork: 0.1611 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8605 / SU B: 6.843 / SU ML: 0.099 / SU R Cruickshank DPI: 0.1516 / SU Rfree: 0.1507 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 1092 9.9 %RANDOM
Rwork0.1626 ---
obs0.1684 11067 99.98 %-
all-11069 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.09 Å2 / Biso mean: 23.0704 Å2 / Biso min: 9.04 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å20.53 Å2
2---1.25 Å20 Å2
3---2.84 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1031 0 26 96 1153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221109
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9981505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5825140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5162550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79715211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.49155
X-RAY DIFFRACTIONr_chiral_restr0.110.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021819
X-RAY DIFFRACTIONr_mcbond_it1.0461.5657
X-RAY DIFFRACTIONr_mcangle_it1.68821057
X-RAY DIFFRACTIONr_scbond_it2.9933452
X-RAY DIFFRACTIONr_scangle_it4.3994.5442
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 72 -
Rwork0.192 752 -
all-824 -
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)
11.2854-0.4599-0.37613.05290.78730.5043-0.09770.067-0.1990.02020.0942-0.0327-0.01610.08330.00350.08860.0132-0.00320.0720.0080.112612.7226-18.33253.0994
20.862-1.92070.57724.2963-1.2850.38680.01060.00480.0637-0.0977-0.0168-0.19630.02870.00420.00630.05430.02060.02620.0709-0.0540.2216.6349-16.72850.8088
32.7479-0.2991-0.31442.43970.19011.0432-0.0668-0.3348-0.0310.26160.0573-0.06940.03810.04370.00960.10550.0145-0.01390.14790.03610.101610.3228-10.76598.9884
42.3411-0.29940.15861.99930.24131.02520.00050.06850.0071-0.08430.03310.0669-0.0241-0.0232-0.03360.065-0.00040.00460.06130.01410.06347.8752-7.48061.3604
52.9365-1.01721.72162.77520.46874.9458-0.2575-0.52760.30350.36020.12350.292-0.2422-0.20430.1340.06710.03540.03720.1113-0.05660.1337-0.71620.594111.0248
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 27
2X-RAY DIFFRACTION2A28 - 36
3X-RAY DIFFRACTION3A37 - 74
4X-RAY DIFFRACTION4A75 - 117
5X-RAY DIFFRACTION5A118 - 135

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