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- PDB-4df7: Crystal structure of Staphylococcal nuclease variant Delta+PHS V2... -

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Basic information

Entry
Database: PDB / ID: 4df7
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS V23L/V99I at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant / pdtp / cavity / pressure
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
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsCaro, J.A. / Schlessman, J.L. / Heroux, A. / 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
DepositionJan 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 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_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)16,6143
Polymers16,1721
Non-polymers4422
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.041, 60.664, 38.239
Angle α, β, γ (deg.)90.000, 93.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16171.518 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: V23L,G50F,V51N,V99I,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.: 95 / 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: 44.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 21% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 22464 / Num. obs: 22464 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.042 / Χ2: 1.419 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.5-1.534.80.2185.310101.01388.8
1.53-1.5550.22510610.96592.6
1.55-1.585.10.20610740.96895.6
1.58-1.625.60.18110920.96998.4
1.62-1.655.90.16111370.93199.1
1.65-1.695.90.14811330.9499.8
1.69-1.736.50.13211370.94100
1.73-1.786.40.11411211.008100
1.78-1.836.10.09411651.067100
1.83-1.896.50.08211081.143100
1.89-1.966.30.06811361.277100
1.96-2.046.30.06511291.481100
2.04-2.136.60.05411481.563100
2.13-2.246.30.04711431.6100
2.24-2.386.50.04411351.636100
2.38-2.566.30.0411461.73299.9
2.56-2.826.80.03811381.93100
2.82-3.236.30.03311391.99499.8
3.23-4.076.40.03411402.06899.5
4.07-506.30.03911722.50899.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.98 Å
Translation2.5 Å30.98 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.2.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BDC

3bdc


Resolution: 1.5→30.98 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.2392 / WRfactor Rwork: 0.1986 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7888 / SU B: 3.862 / SU ML: 0.069 / SU R Cruickshank DPI: 0.0807 / SU Rfree: 0.0849 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.081 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 2207 9.9 %RANDOM
Rwork0.1859 ---
all0.1895 22399 --
obs0.1895 22399 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.93 Å2 / Biso mean: 27.8839 Å2 / Biso min: 14.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å20.82 Å2
2---1.77 Å20 Å2
3---3.68 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 26 95 1156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221123
X-RAY DIFFRACTIONr_angle_refined_deg1.8082.0081522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46425.10249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09915222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.87155
X-RAY DIFFRACTIONr_chiral_restr0.1330.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021817
X-RAY DIFFRACTIONr_mcbond_it1.7441.5662
X-RAY DIFFRACTIONr_mcangle_it2.44821068
X-RAY DIFFRACTIONr_scbond_it3.3633461
X-RAY DIFFRACTIONr_scangle_it4.8844.5448
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 149 -
Rwork0.304 1356 -
all-1505 -
obs-1505 89.26 %
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)
11.773-0.0738-0.5163.7240.54941.1899-0.0353-0.0563-0.24430.09080.0235-0.02480.11030.02750.01180.1130.01570.00350.09690.0090.124112.0419-3.21513.9163
21.4775-2.3509-0.28966.23870.98890.4324-0.05210.0452-0.1860.04760.0771-0.06320.10990.077-0.0250.10660.01160.00160.0996-0.00780.107915.3831-1.82221.291
32.4206-0.00270.07752.6160.45621.9315-0.0122-0.2598-0.04340.28040.0048-0.03320.07460.03040.00740.11340.0130.00970.13060.01880.11310.32732.62399.4127
42.906-0.4049-0.09262.08150.35190.8819-0.00230.10170.096-0.0660.00590.0808-0.0159-0.0663-0.00360.0884-0.0027-0.00610.080.00810.07357.33947.13921.5609
55.63172.06973.2962.6060.90916.5864-0.0663-0.67350.55180.36890.00170.256-0.2697-0.21360.06450.09430.05310.03440.1247-0.07050.1869-1.206115.596112.8165
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 22
2X-RAY DIFFRACTION2A23 - 39
3X-RAY DIFFRACTION3A40 - 80
4X-RAY DIFFRACTION4A81 - 126
5X-RAY DIFFRACTION5A127 - 141

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