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- PDB-3va5: Crystal structure of Staphylococcal nuclease variant Delta+PHS I9... -

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Basic information

Entry
Database: PDB / ID: 3va5
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS I92A/V23A at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant / pdtp / pressure / cavity
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 / molecular replacement / Resolution: 1.55 Å
AuthorsCaro, J.A. / Nam, S.P. / Heroux, A. / Schlessman, J.L. / Garcia-Moreno, E.B.
CitationJournal: To be Published
Title: Pressure effects in proteins.
Authors: Caro, J.A. / Schlessman, J.L. / Garcia-Moreno, E.B.
History
DepositionDec 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_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)16,5163
Polymers16,0731
Non-polymers4422
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.179, 60.266, 38.100
Angle α, β, γ (deg.)90.00, 94.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16073.330 Da / Num. of mol.: 1 / Fragment: unp residues 83-231
Mutation: V102A, G50F,V51N,I92A,L103A,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-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.: 111 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% 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: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 20327 / Num. obs: 20327 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.066 / Χ2: 2.07 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.55-1.584.20.3363.58650.95285.9
1.58-1.614.50.3019431.02291.3
1.61-1.6450.2659861.08995.5
1.64-1.675.50.25510181.18598.5
1.67-1.715.90.24210231.17899.4
1.71-1.7560.22810321.19100
1.75-1.795.80.19610071.448100
1.79-1.846.20.16510731.458100
1.84-1.8960.1559991.70799.7
1.89-1.956.10.12610271.85899.8
1.95-2.026.20.11710482.032100
2.02-2.15.90.09610142.31699.7
2.1-2.25.90.0910292.41399.5
2.2-2.325.90.0810222.39399.3
2.32-2.466.30.07510342.53799.5
2.46-2.6560.06510462.57299.7
2.65-2.9260.06310292.84699.9
2.92-3.3460.05610383.1599.1
3.34-4.215.70.05210373.2998.8
4.21-505.80.05810573.63798.3

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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
SCALEPACKdata scaling
PHASER2.2.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3BDC

3bdc


Resolution: 1.55→32.12 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.2249 / WRfactor Rwork: 0.1814 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8523 / SU B: 3.234 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0851 / SU Rfree: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.085 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 2046 10.2 %RANDOM
Rwork0.1751 ---
all0.1793 20146 --
obs0.1793 20146 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.63 Å2 / Biso mean: 26.3955 Å2 / Biso min: 13.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å21.01 Å2
2---1.01 Å20 Å2
3---2.75 Å2
Refinement stepCycle: LAST / Resolution: 1.55→32.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1028 0 26 111 1165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221118
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.9991513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1345141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9852550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57715220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.054155
X-RAY DIFFRACTIONr_chiral_restr0.1620.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021819
X-RAY DIFFRACTIONr_mcbond_it1.4591.5659
X-RAY DIFFRACTIONr_mcangle_it2.16321058
X-RAY DIFFRACTIONr_scbond_it3.2223459
X-RAY DIFFRACTIONr_scangle_it4.9174.5448
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 138 -
Rwork0.311 1208 -
all-1346 -
obs-1346 89.97 %
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)
12.4602-0.46660.23663.54420.77620.7701-0.0411-0.0144-0.26110.12280.08780.00450.07930.1138-0.04670.09180.0040.02750.10950.01450.118212.238530.26443.3411
21.6303-1.9395-0.49215.67121.52490.41460.06260.0504-0.1022-0.0335-0.0329-0.1998-0.0037-0.0192-0.02970.09190.01490.03150.1007-0.00960.158717.173328.77670.0401
32.03120.027-0.30182.628-0.0770.7956-0.0474-0.4080.10240.42890.0657-0.06210.13170.0774-0.01830.1470.01970.00040.155-0.0060.053311.286839.172913.5706
42.3838-0.59930.19445.9902-1.15542.65480.02540.1626-0.267-0.0914-0.11430.1971-0.0015-0.00890.08890.124-0.00480.01470.1337-0.01550.15787.667231.1934-2.1029
52.81030.031-0.01612.57730.07910.4742-0.05930.1982-0.1007-0.08240.05410.00510.09540.0120.00520.1259-0.00490.01410.1344-0.00330.133712.318435.6623-0.2038
62.7216-0.1810.18032.38680.22310.7882-0.01670.04860.1463-0.05030.03140.212-0.0455-0.0791-0.01470.0990.00320.00830.11740.00410.13574.352243.51532.5566
73.9268-0.24871.15973.7290.32395.0997-0.1337-0.4280.3720.42640.08990.2932-0.2386-0.26110.04380.08450.02640.05470.0971-0.04540.1215-0.805348.62211.9102
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 24
2X-RAY DIFFRACTION2A25 - 35
3X-RAY DIFFRACTION3A36 - 69
4X-RAY DIFFRACTION4A70 - 80
5X-RAY DIFFRACTION5A81 - 97
6X-RAY DIFFRACTION6A98 - 124
7X-RAY DIFFRACTION7A125 - 141

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