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- PDB-3oso: Crystal structure of Staphylococcal nuclease variant Delta+PHS L2... -

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Basic information

Entry
Database: PDB / ID: 3oso
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS L25A 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionSep 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Sep 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)16,5443
Polymers16,1011
Non-polymers4422
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.143, 60.252, 38.013
Angle α, β, γ (deg.)90.00, 94.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thermonuclease


Mass: 16101.383 Da / Num. of mol.: 1 / Fragment: Deletion UNP residues 126-131 / Mutation: L25A, G132P, V133N, P199G, H206L, 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
#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.: 100 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 7.0, 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 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 Å / Relative weight: 1
ReflectionResolution: 1.35→60 Å / Num. all: 27209 / Num. obs: 27209 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.35-1.373.20.583136.4
1.37-1.43.80.522148.8
1.4-1.434.20.457160.7
1.43-1.454.70.437173
1.45-1.495.30.393179.7
1.49-1.525.60.343187.5
1.52-1.566.30.335194.9
1.56-1.66.80.307197.8
1.6-1.657.20.237199
1.65-1.77.30.199199.2
1.7-1.767.40.168199.2
1.76-1.837.30.128199.2
1.83-1.927.40.101199.7
1.92-2.027.30.074199.5
2.02-2.147.40.059199.7
2.14-2.317.30.052199.7
2.31-2.547.30.049199.9
2.54-2.917.20.0451100
2.91-3.666.90.033199.2
3.66-607.30.029197.7

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Phasing

Phasing MRRfactor: 37.42 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å25.08 Å
Translation2.5 Å25.08 Å

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Processing

Software
NameVersionClassificationNB
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 H20s, Ca2+ and THP removed and the following truncations: H8A, T13A, L25A, Q30A, K64A, Q80A, T82A, M98A, Y113A, V114A, Y115A, K116A, Q131A, K134A and K136A; all b- ...Starting model: 3BDC with all H20s, Ca2+ and THP removed and the following truncations: H8A, T13A, L25A, Q30A, K64A, Q80A, T82A, M98A, Y113A, V114A, Y115A, K116A, Q131A, K134A and K136A; all b-factors were reset to 20 A2.

3bdc


Resolution: 1.6→30.13 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.701 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0924 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20588 1831 9.9 %RANDOM
Rwork0.16714 ---
obs0.1709 16596 99.38 %-
all-18427 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.281 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20.76 Å2
2---0.93 Å20 Å2
3---2.25 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 26 100 1156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221113
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.781.9981507
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9585140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04824.89849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46915218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.274155
X-RAY DIFFRACTIONr_chiral_restr0.1520.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021815
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3921.5657
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.20421058
X-RAY DIFFRACTIONr_scbond_it3.2353456
X-RAY DIFFRACTIONr_scangle_it4.894.5443
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 136 -
Rwork0.189 1232 -
obs--98.99 %
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)
11.6889-0.6085-0.35752.3450.50070.2596-0.0538-0.1058-0.16280.08810.05210.01040.05290.08390.00180.11740.0127-0.00860.11150.01770.093413.8788-0.51523.4134
23.26470.3661-0.18598.36522.44583.1261-0.1293-0.6281-0.10490.56130.1102-0.0620.12380.16510.01910.18720.03730.00250.21010.03490.006710.64054.29916.332
32.3363-0.52640.16532.03060.55190.3243-0.06360.1589-0.1557-0.00670.01120.12730.0361-0.02730.05240.1237-0.0054-0.00590.10360.00020.09378.94631.27620.7596
45.13730.1893-2.29193.1785-0.93473.1334-0.07830.04480.22-0.02280.09270.06690.0242-0.1014-0.01450.1210.0008-0.0220.1173-0.00420.11516.69612.96924.5901
52.8239-0.71360.02632.38910.3831.8722-0.0603-0.22930.20780.13930.08210.2833-0.1987-0.0198-0.02180.09670.00380.01020.0983-0.00720.13010.07213.72637.0872
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 43
2X-RAY DIFFRACTION2A50 - 62
3X-RAY DIFFRACTION3A63 - 98
4X-RAY DIFFRACTION4A99 - 110
5X-RAY DIFFRACTION5A111 - 135

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