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- PDB-4laa: Crystal structure of Staphylococcal nuclease variant Delta+PHS L3... -

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Basic information

Entry
Database: PDB / ID: 4laa
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS L36H at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / nuclease / hyperstable / pdTp / ionizable group
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: 1.58 Å
AuthorsWheeler, E.L. / Schlessman, J.L. / Heroux, A. / Garcia-Moreno E., B. / Robinson, A.C.
CitationJournal: To be Published
Title: Crystal structure of Staphylococcal nuclease variant Delta+PHS L36H at cryogenic temperature
Authors: Wheeler, E.L. / Schlessman, J.L. / Heroux, A. / Garcia-Moreno E., B. / Robinson, A.C. / Sorenson, J.L.
History
DepositionJun 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: 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

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Assembly

Deposited unit
A: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6113
Polymers16,1681
Non-polymers4422
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.048, 60.326, 38.202
Angle α, β, γ (deg.)90.000, 93.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16168.453 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: L36H/G50F/V51N/P117G/H124L/S128A/Del44-49
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, micrococcal nuclease
#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.: 89 / 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: 44.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 8, 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: Jun 3, 2013
Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. all: 19399 / Num. obs: 19399 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.059 / Χ2: 1.464 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.58-1.616.30.30869480.95499.9
1.61-1.646.50.2519710.953100
1.64-1.676.50.2479570.976100
1.67-1.76.30.2199661.05100
1.7-1.746.70.1979781.049100
1.74-1.786.70.1649481.069100
1.78-1.826.70.1389841.08100
1.82-1.876.30.1239551.198100
1.87-1.936.60.1119761.286100
1.93-1.996.70.0979541.368100
1.99-2.066.50.0859711.403100
2.06-2.146.80.0789541.465100
2.14-2.246.80.079891.524100
2.24-2.366.70.0679561.591100
2.36-2.516.50.0639761.623100
2.51-2.76.80.069671.78100
2.7-2.976.70.0569861.893100
2.97-3.46.80.0519742.14399.9
3.4-4.296.60.059842.341100
4.29-506.40.04810052.383100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.14 Å
Translation2.5 Å38.14 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BDC

3bdc


Resolution: 1.58→38.14 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.2004 / WRfactor Rwork: 0.1804 / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8876 / SU B: 2.385 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0823 / SU Rfree: 0.0784 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.082 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1907 987 5.1 %RANDOM
Rwork0.1721 ---
all0.173 0 --
obs0.173 19334 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.51 Å2 / Biso mean: 23.7812 Å2 / Biso min: 12.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.05 Å2
2---0.03 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.58→38.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 26 89 1150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021139
X-RAY DIFFRACTIONr_angle_refined_deg1.9791.9921548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1815146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1332552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61415224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.996155
X-RAY DIFFRACTIONr_chiral_restr0.1430.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021841
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 61 -
Rwork0.199 1318 -
all-1379 -
obs-1318 99.93 %
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)
11.4885-0.3674-0.22642.55530.37540.5047-0.0431-0.0072-0.1509-0.0080.074-0.04860.10350.0603-0.03080.0770.0156-0.00890.06780.00630.046913.628-1.782.967
24.08132.00381.448810.4072.27573.7148-0.1241-0.50390.00780.58970.0978-0.10680.0410.23840.02630.15160.0338-0.00440.17280.01980.009311.5134.23416.199
33.67070.7208-0.80727.1786-2.91886.9011-0.01280.2172-0.2975-0.0702-0.04280.16170.03810.00240.05560.1033-0.0047-0.01760.0978-0.02360.08737.785-2.868-1.516
41.9829-0.34530.40252.38250.18930.3676-0.07220.0222-0.0850.05470.06710.13130.0848-0.01740.0050.08430.0014-0.00560.07890.01420.06178.5073.6543.737
53.8354-0.48970.18933.75770.47952.04640.00160.34270.1548-0.33430.00140.1189-0.1337-0.0418-0.0030.1169-0.0021-0.02310.10930.0390.09056.20211.996-2.155
63.3872-0.56981.43783.63760.13765.1346-0.193-0.39790.24970.39550.13260.3439-0.3119-0.22860.06040.07050.03650.04220.0764-0.0190.1059-0.89314.69611.227
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 42
2X-RAY DIFFRACTION2A43 - 69
3X-RAY DIFFRACTION3A70 - 80
4X-RAY DIFFRACTION4A81 - 108
5X-RAY DIFFRACTION5A109 - 123
6X-RAY DIFFRACTION6A124 - 141

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