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- PDB-5c4z: Crystal structure of Staphylococcal nuclease variant Delta+PHS L2... -

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Basic information

Entry
Database: PDB / ID: 5c4z
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS L25H 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å
AuthorsSorenson, J.L. / Schlessman, J.L. / Garcia-Moreno E., B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM061597 United States
CitationJournal: To be Published
Title: Crystal structure of Staphylococcal nuclease variant Delta+PHS L25H at cryogenic temperature
Authors: Sorenson, J.L. / Schlessman, J.L. / Garcia-Moreno E., B.
History
DepositionJun 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)16,6113
Polymers16,1681
Non-polymers4422
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-14 kcal/mol
Surface area6840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.039, 60.511, 38.111
Angle α, β, γ (deg.)90.000, 93.950, 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: UNP residues 83-231 / Mutation: L25H/G50F/V51N/P117G/H124L/S128A/Del44-49
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: pET24a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 126 / 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: 44.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 30% MPD, 25 mM potassium phosphate, calcium chloride, pdTp

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Apr 17, 2015 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. all: 17960 / Num. obs: 17960 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.79 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.0212 / Net I/σ(I): 32.13 / Num. measured all: 215598
Reflection shellResolution: 1.62→1.64 Å / Redundancy: 6.38 % / Rmerge(I) obs: 0.1755 / Mean I/σ(I) obs: 5.41 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.62 Å32.19 Å
Translation1.62 Å32.19 Å

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Processing

Software
NameVersionClassification
SAINTdata scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BDC

3bdc


Resolution: 1.62→32.19 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.191 / WRfactor Rwork: 0.1667 / FOM work R set: 0.8758 / SU B: 2.705 / SU ML: 0.057 / SU R Cruickshank DPI: 0.0901 / SU Rfree: 0.0863 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1922 916 5.1 %RANDOM
Rwork0.1682 ---
obs0.1694 17023 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.03 Å2 / Biso mean: 17.703 Å2 / Biso min: 7.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.07 Å2
2---0.1 Å20 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 1.62→32.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 26 126 1187
Biso mean--10.06 23.68 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191170
X-RAY DIFFRACTIONr_bond_other_d0.0010.021193
X-RAY DIFFRACTIONr_angle_refined_deg1.9332.0031593
X-RAY DIFFRACTIONr_angle_other_deg0.83732776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0295156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03325.09851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72715244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.211155
X-RAY DIFFRACTIONr_chiral_restr0.1260.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021297
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02254
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 75 -
Rwork0.182 1244 -
all-1319 -
obs--100 %
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)
14.69782.38912.02969.6477-2.44662.48920.02590.4557-0.4455-0.08940.25150.62150.03260.1384-0.27740.05270.0052-0.01290.1166-0.12950.4552.743-5.452232.9927
20.6205-0.1167-0.13141.23090.27840.0815-0.0231-0.0591-0.0360.02810.0261-0.07220.01060.0158-0.0030.07720.0185-0.00550.0832-0.00010.065112.7613-0.163643.2904
31.21120.46480.18053.95371.3690.7031-0.1461-0.4273-0.08920.29970.10890.1550.13910.03980.03710.13580.0490.02040.18220.04680.01747.42422.655753.4178
41.2124-0.4614-0.10631.30420.22490.1747-0.02880.0494-0.013-0.03810.010.10720.012-0.01130.01880.0549-0.0066-0.00110.07570.0010.05233.78136.444139.1651
517.48950.17850.93411.42771.60723.1199-0.1779-0.32840.72990.26370.00820.0691-0.3328-0.21720.16970.3580.0893-0.00820.0818-0.06430.0769-2.130216.65353.1451
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 11
2X-RAY DIFFRACTION2A12 - 50
3X-RAY DIFFRACTION3A51 - 71
4X-RAY DIFFRACTION4A72 - 131
5X-RAY DIFFRACTION5A132 - 141

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