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- PDB-4hth: Crystal structure of Staphylococcal nuclease variant Delta+VIAGLA... -

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Basic information

Entry
Database: PDB / ID: 4hth
TitleCrystal structure of Staphylococcal nuclease variant Delta+VIAGLA at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / nuclease / hyperstable / pdTp
Function / homology
Function and homology information


endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / membrane / metal ion binding
Similarity search - Function
Thermonuclease family signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / 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) ...Thermonuclease family signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / 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: 1.75 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+VIAGLA at cryogenic temperature
Authors: Wheeler, E.L. / Schlessman, J.L. / Robinson, A.C. / Garcia-Moreno E., B.
History
DepositionNov 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: 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 / 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 / _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)16,5402
Polymers16,1381
Non-polymers4021
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.181, 60.464, 38.385
Angle α, β, γ (deg.)90.00, 94.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16137.545 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231)
Mutation: T33V/T41I/G50V/V51N/S59A/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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 44.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 42% MPD, 25 mM potassium phosphate, with protein:pdTp:calcium chloride in 1:2:3 molar equivalent ratio, pH 6, 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 28, 2011
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: 1.75→50 Å / Num. all: 14298 / Num. obs: 14298 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 50.185
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 4.109 / % possible all: 96.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.28 Å
Translation2.5 Å38.28 Å

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Processing

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

3bdc


Resolution: 1.75→31.1 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.279 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1135 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20921 719 5 %RANDOM
Rwork0.17535 ---
obs0.17703 13559 99.17 %-
all-14278 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.931 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20.18 Å2
2---0.19 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.75→31.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1033 0 25 70 1128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021125
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.9981525
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8215143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5552550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24315218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.055155
X-RAY DIFFRACTIONr_chiral_restr0.1560.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021831
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 44 -
Rwork0.21 941 -
obs--95.63 %
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)
11.7852-0.4-0.33553.23220.53670.2746-0.0145-0.0049-0.2334-0.02260.0386-0.06060.03070.0485-0.02420.09880.0109-0.02990.10740.00430.085413.858-3.7492.172
28.13173.72674.82863.94863.201612.1438-0.0087-0.64730.45840.6263-0.3931-0.0515-0.30660.7760.40180.2353-0.0915-0.10710.28920.01020.091414.08212.40312.927
32.72140.1234-0.20582.11030.27851.5394-0.0171-0.0367-0.19020.08250.02950.03310.0797-0.063-0.01250.13450.0088-0.02660.13150.01440.094110.4940.5924.454
42.1327-3.6827-2.008210.32674.28175.1755-0.1773-0.2527-0.14360.41960.09890.59760.3615-0.1470.07840.0951-0.00360.02110.17080.02330.12151.8824.6898.898
54.0453-0.90260.31292.55630.70791.05090.00830.28430.223-0.20280.01780.0697-0.1685-0.007-0.02610.0693-0.0033-0.02940.09640.02660.05194.33211.814-0.457
611.64491.2326.46737.14950.243911.9693-0.1662-0.72740.77450.50890.31140.6288-0.5379-0.5485-0.14520.09050.0590.05890.1684-0.04790.1453-0.75315.63514.299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 37
2X-RAY DIFFRACTION2A38 - 53
3X-RAY DIFFRACTION3A54 - 95
4X-RAY DIFFRACTION4A96 - 107
5X-RAY DIFFRACTION5A108 - 128
6X-RAY DIFFRACTION6A129 - 141

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