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- PDB-4r8n: Crystal structure of Staphylococcal nuclease variant V23I/V66I/I7... -

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Basic information

Entry
Database: PDB / ID: 4r8n
TitleCrystal structure of Staphylococcal nuclease variant V23I/V66I/I72V/I92V at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / 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
PHOSPHATE ION / THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsCaro, J.A. / Flores, E. / Schlessman, J.L. / Heroux, A. / Garcia-Moreno, E.B.
CitationJournal: To be Published
Title: Cavities in proteins
Authors: Caro, J.A. / Schlessman, J.L. / Garcia-Moreno, E.B.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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)16,6825
Polymers16,0271
Non-polymers6554
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.605, 47.605, 62.912
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thermonuclease / TNase / Micrococcal nuclease / Staphylococcal nuclease / Nuclease B / Nuclease A


Mass: 16026.601 Da / Num. of mol.: 1 / Fragment: UNP residues 83-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Production host: Escherichia coli (E. coli) / References: UniProt: P00644, micrococcal nuclease

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Non-polymers , 5 types, 77 molecules

#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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 44.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 20% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2013
RadiationMonochromator: Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. ...Monochromator: Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. Mirror: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 16933 / Num. obs: 16933 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.041 / Χ2: 1.557 / Net I/σ(I): 20.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.65-1.6813.10.27412.18261.09100
1.68-1.7113.20.268351.079100
1.71-1.7412.80.1978431.121100
1.74-1.7812.30.1588481.181100
1.78-1.8213.40.1428451.228100
1.82-1.8613.40.1268231.21100
1.86-1.913.30.1088681.32100
1.9-1.9612.80.0818231.357100
1.96-2.0112.50.0718461.383100
2.01-2.0813.40.0618401.4100
2.08-2.15130.0548601.532100
2.15-2.2412.50.058521.603100
2.24-2.3413.70.0478301.739100
2.34-2.4613.30.0438521.813100
2.46-2.6212.60.0368471.732100
2.62-2.8213.30.0368531.861100
2.82-3.1112.70.0318411.81100
3.11-3.5513.50.038631.839100
3.55-4.4812.80.0368582.082100
4.48-5012.30.0448802.75299.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.96 Å
Translation2.5 Å37.96 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SNC

1snc


Resolution: 1.65→47.6 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2653 / WRfactor Rwork: 0.2139 / FOM work R set: 0.8195 / SU B: 4.917 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1059 / SU Rfree: 0.1092 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 852 5 %RANDOM
Rwork0.1941 ---
all0.1963 16911 --
obs0.1963 16911 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.28 Å2 / Biso mean: 36.702 Å2 / Biso min: 16.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2--0.71 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.65→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 39 73 1172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021139
X-RAY DIFFRACTIONr_angle_refined_deg1.8872.0161542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4145138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73524.68147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2415220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.685155
X-RAY DIFFRACTIONr_chiral_restr0.1240.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021814
LS refinement shellResolution: 1.651→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 59 -
Rwork0.277 1150 -
all-1209 -
obs-1209 98.61 %
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)
13.9231-0.5944-2.2175.0585-1.08136.20230.3773-0.2974-0.1335-0.3075-0.1191-0.4059-0.19480.8231-0.25820.1833-0.08-0.02270.264-0.00150.1114-9.8481-3.3086-0.2441
25.2307-0.3904-2.70722.9054-0.03155.14311.0366-0.32020.8219-0.2615-0.1857-0.1575-1.62860.2255-0.85080.6468-0.13020.2590.1796-0.02930.1983-16.85910.58774.0628
32.9952-0.4991-2.15362.45940.0677.20440.1123-0.2761-0.1783-0.16570.03080.0388-0.15910.3856-0.14320.1466-0.0509-0.0470.18530.03130.0897-15.8903-3.65340.7199
42.5163-0.7422-2.30972.29472.10618.40630.44240.1707-0.1176-0.2149-0.16180.3417-1.1457-1.0429-0.28060.29180.10330.01510.29980.07940.1351-28.27083.5585.7713
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 32
2X-RAY DIFFRACTION2A33 - 63
3X-RAY DIFFRACTION3A64 - 97
4X-RAY DIFFRACTION4A98 - 141

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