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- PDB-3p1h: Crystal structure of Staphylococcal nuclease variant Delta+PHS V2... -

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Basic information

Entry
Database: PDB / ID: 3p1h
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS V23K/I92A at cryogenic temperature
Componentsthermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant / pdtp / pressure sensitivity / cavity
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: 1.79 Å
AuthorsClark, I.A. / Caro, J.A. / Sue, G. / Schlessman, J.L. / Garcia-Moreno E, B. / Heroux, A.
CitationJournal: To be Published
Title: Pressure unfolding effects of artificial cavities in proteins.
Authors: Caro, J.A. / Clark, I.A. / Sue, G. / Schlessman, J.L. / Garcia-Moreno E, B.
History
DepositionSep 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Atomic model
Revision 1.2Sep 6, 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)16,5743
Polymers16,1311
Non-polymers4422
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.131, 60.448, 37.972
Angle α, β, γ (deg.)90.000, 93.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein thermonuclease


Mass: 16131.434 Da / Num. of mol.: 1 / Fragment: Deletion UNP residues 126-131 / Mutation: V23K,G50F,V51N,I92A,P117G,H124L,S128A
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.: 61 / 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: 44.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 27% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2009 / Details: mirrors
RadiationMonochromator: Double sillicon (111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 13067 / Num. obs: 13067 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 31.26 Å2 / Rmerge(I) obs: 0.075 / Χ2: 2.025 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.79-1.8212.40.286491.051197
1.82-1.8512.50.286171.08197.9
1.85-1.8912.50.2466641.196197.2
1.89-1.9312.50.2116541.273198.3
1.93-1.9712.30.1796461.293197.9
1.97-2.0212.30.1746421.305197.6
2.02-2.0712.40.146601.573198.5
2.07-2.1212.20.1276471.604198.6
2.12-2.1812.30.1126461.692198.2
2.18-2.2612.10.1036581.786198.1
2.26-2.34120.0976521.866198.6
2.34-2.43120.0916551.98198.9
2.43-2.5411.80.0846772.185199
2.54-2.6711.80.0766432.379198.9
2.67-2.8411.60.0746762.507199.4
2.84-3.0611.30.0686502.912198.9
3.06-3.3710.90.0636753.193199.4
3.37-3.8610.20.0576743.513199.6
3.86-4.8610.50.0556563.648197.5
4.86-509.90.0556263.527189.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.14 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å21.76 Å
Translation2.5 Å21.76 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 3BDC Residues 7-141, deleted waters and cofactors, all B factors set to 20.00 A2, truncated: H8A, T13A, V23A, Q30A, K64A, T82A, I92A, Y113A, V114A, Y115A

3bdc


Resolution: 1.79→22.94 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2316 / WRfactor Rwork: 0.183 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8548 / SU B: 5.096 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1331 / SU Rfree: 0.1341 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 1298 10 %RANDOM
Rwork0.1791 ---
all0.1841 13040 --
obs0.1841 13040 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.41 Å2 / Biso mean: 24.8326 Å2 / Biso min: 11.54 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å20.37 Å2
2---1.31 Å20 Å2
3---3.12 Å2
Refinement stepCycle: LAST / Resolution: 1.79→22.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 26 61 1119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221101
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9991485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.375134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.72424.89849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06215214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.262155
X-RAY DIFFRACTIONr_chiral_restr0.1220.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021807
X-RAY DIFFRACTIONr_mcbond_it1.2521.5651
X-RAY DIFFRACTIONr_mcangle_it1.94621042
X-RAY DIFFRACTIONr_scbond_it3.273450
X-RAY DIFFRACTIONr_scangle_it4.7154.5441
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 93 -
Rwork0.233 864 -
all-957 -
obs--96.96 %
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)
11.5736-0.8691-0.10463.0370.38290.1979-0.0517-0.0075-0.10850.02970.0926-0.05790.08330.0424-0.04090.08020.00850.00940.07180.00940.081413.4366-1.44212.8126
22.59162.9791.478811.58283.65184.4043-0.1796-0.5207-0.22420.17220.1312-0.6113-0.09820.45180.04850.08580.0308-0.04610.27420.01730.013514.272611.063917.3611
31.8617-0.00790.51912.35730.78140.6375-0.048-0.0111-0.30110.20360.01930.04670.167-0.10110.02870.10310.00730.01550.06340.03830.11138.0108-2.51065.5564
42.087-0.90050.04382.24120.44730.3438-0.02590.0770.0548-0.06980.06290.03610.02480.0317-0.03690.0588-0.01060.00850.07510.01580.06277.61766.80541.7876
510.4388-0.37186.12512.4456-1.11047.8102-0.0509-0.19890.24830.33060.1030.33340.05040.1477-0.05210.06910.05170.04130.0473-0.03340.0786-0.538314.909411.1618
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 42
2X-RAY DIFFRACTION2A43 - 59
3X-RAY DIFFRACTION3A60 - 80
4X-RAY DIFFRACTION4A81 - 123
5X-RAY DIFFRACTION5A124 - 141

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