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- PDB-4dfa: Crystal structure of Staphylococcal nuclease variant Delta+PHS I9... -

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Basic information

Entry
Database: PDB / ID: 4dfa
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS I92A/L36A 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: 1.404 Å
AuthorsCaro, J.A. / Clark, I.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)16,5023
Polymers16,0591
Non-polymers4422
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.113, 60.446, 38.309
Angle α, β, γ (deg.)90.000, 93.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16059.303 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: L36A,G50F,V51N,I92A,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.: 130 / 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: 2.24 Å3/Da / Density % sol: 45.04 %
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: 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: 1.404→50 Å / Num. all: 27015 / Num. obs: 27015 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.05 / Χ2: 1.502 / Net I/σ(I): 14.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.404-1.434.40.2585.411880.92987.2
1.43-1.464.90.22712500.88691
1.46-1.495.40.21413340.87696.5
1.49-1.5260.17613090.81298.1
1.52-1.556.10.16913790.80898.9
1.55-1.595.90.14513440.87899.4
1.59-1.636.40.12113530.94199.3
1.63-1.676.20.10513680.9699.3
1.67-1.726.50.09613620.97299.6
1.72-1.786.40.08413601.04499.7
1.78-1.846.10.07114001.14699.7
1.84-1.916.60.06913361.37799.9
1.91-26.10.06113621.56599.9
2-2.116.60.05513821.747100
2.11-2.246.40.0513841.981100
2.24-2.416.40.04813861.998100
2.41-2.656.30.04313682.11199.9
2.65-3.046.60.04213682.30699.7
3.04-3.836.10.04213792.72598.9
3.83-506.30.04914033.18798.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.22 Å
Translation2.5 Å38.22 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: 1.404→38.22 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.2074 / WRfactor Rwork: 0.1743 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8745 / SU B: 1.973 / SU ML: 0.04 / SU R Cruickshank DPI: 0.058 / SU Rfree: 0.0597 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.058 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1876 1356 5 %RANDOM
Rwork0.1635 ---
all0.1647 27001 --
obs0.1647 27001 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.02 Å2 / Biso mean: 24.2695 Å2 / Biso min: 11.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20.74 Å2
2---1.56 Å20 Å2
3---2.55 Å2
Refinement stepCycle: LAST / Resolution: 1.404→38.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1027 0 26 130 1183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221153
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.9991569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.345153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6192550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94315234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.241155
X-RAY DIFFRACTIONr_chiral_restr0.1380.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021843
X-RAY DIFFRACTIONr_mcbond_it1.391.5677
X-RAY DIFFRACTIONr_mcangle_it2.17521098
X-RAY DIFFRACTIONr_scbond_it3.3643476
X-RAY DIFFRACTIONr_scangle_it4.9694.5458
LS refinement shellResolution: 1.404→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 73 -
Rwork0.295 1487 -
all-1560 -
obs-1560 77.11 %
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)
14.15-1.39860.81359.4507-4.30515.3649-0.01910.5045-0.9335-0.4650.09520.66160.0484-0.1117-0.07610.0823-0.0084-0.02140.0876-0.08560.35645.9186-80.8026-4.2637
21.9064-1.0488-0.69513.54641.58630.984-0.1031-0.1182-0.26880.16480.1214-0.2030.0820.0945-0.01830.12520.02620.00010.11290.01660.180916.8716-79.09424.71
33.2263-0.2604-0.27623.24220.41451.0821-0.0831-0.3298-0.09060.36250.04460.02920.13910.06170.03850.15610.01390.010.15440.02210.121910.4008-71.68648.6771
44.3190.1474-0.48113.15770.13340.7041-0.08370.2258-0.2124-0.050.0442-0.07530.06030.00360.03950.12690.00180.00430.1280.00180.139212.3632-72.9085-0.1784
53.1182-0.405-0.13882.67430.51440.7634-0.05850.05980.1911-0.01670.01980.2110.0075-0.05830.03870.09580.00390.00150.10550.00770.17153.5937-64.42683.0292
611.5628-0.11696.12713.8904-1.10316.4249-0.2874-0.74940.70130.57710.15440.4429-0.216-0.31460.1330.17150.04810.06850.1819-0.10490.1934-0.512-59.105214.6159
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 12
2X-RAY DIFFRACTION2A13 - 34
3X-RAY DIFFRACTION3A35 - 80
4X-RAY DIFFRACTION4A81 - 97
5X-RAY DIFFRACTION5A98 - 130
6X-RAY DIFFRACTION6A131 - 141

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