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- PDB-3np8: Crystal structure of Staphylococcal nuclease variant Delta+PHS L3... -

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Basic information

Entry
Database: PDB / ID: 3np8
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS L36A at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant / 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
THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsCaro, J.A. / Schlessman, J.L. / Garcia-Moreno, E.B. / Heroux, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Cavities determine the pressure unfolding of proteins.
Authors: Roche, J. / Caro, J.A. / Norberto, D.R. / Barthe, P. / Roumestand, C. / Schlessman, J.L. / Garcia, A.E. / Garcia-Moreno E, B. / Royer, C.A.
History
DepositionJun 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Sep 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

Downloads & links

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Assembly

Deposited unit
A: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5443
Polymers16,1011
Non-polymers4422
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.011, 60.404, 38.275
Angle α, β, γ (deg.)90.00, 93.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thermonuclease


Mass: 16101.383 Da / Num. of mol.: 1 / Fragment: Deletion UNP residues 126-131 / Mutation: L36A,G50F,V51N,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.: 45 / 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: 44.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 6.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 15463 / Num. obs: 15463 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.04 / Χ2: 1.881 / Net I/σ(I): 21.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.736.10.2537360.969192.6
1.73-1.766.40.2517401.025197.1
1.76-1.796.80.2077841.179199.9
1.79-1.837.10.1828001.1731100
1.83-1.877.30.177281.2691100
1.87-1.917.20.147951.4831100
1.91-1.967.40.1147801.661100
1.96-2.027.30.1087841.681100
2.02-2.077.30.0897732.0181100
2.07-2.147.30.0837692.1121100
2.14-2.227.30.0697932.1761100
2.22-2.317.30.0697712.2981100
2.31-2.417.30.0587862.2511100
2.41-2.547.30.0557792.3621100
2.54-2.77.30.0487672.4581100
2.7-2.917.30.0477772.562199.9
2.91-3.27.20.047952.572199.5
3.2-3.667.10.0357742.51199.5
3.66-4.616.90.0287841.891198.7
4.61-5070.0267481.525191.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.79 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.94 Å
Translation2.5 Å30.94 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: 3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, L36A, Q30A, K64A, T82A, Y113A, V114A, Y115A; all b-factors were reset to 20 A^2.

3bdc


Resolution: 1.7→30.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2411 / WRfactor Rwork: 0.2039 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8499 / SU B: 4.646 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1154 / SU Rfree: 0.1152 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 1540 10 %RANDOM
Rwork0.1894 ---
all0.1894 ---
obs0.1933 15410 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.94 Å2 / Biso mean: 34.2096 Å2 / Biso min: 15.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å20.7 Å2
2---1.32 Å20 Å2
3---2.91 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 26 45 1101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221095
X-RAY DIFFRACTIONr_angle_refined_deg1.6772.0011482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5895136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86224.89447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19415211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.858155
X-RAY DIFFRACTIONr_chiral_restr0.1280.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021797
X-RAY DIFFRACTIONr_mcbond_it1.3531.5651
X-RAY DIFFRACTIONr_mcangle_it1.97721048
X-RAY DIFFRACTIONr_scbond_it3.3323444
X-RAY DIFFRACTIONr_scangle_it4.434.5430
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 109 -
Rwork0.277 963 -
all-1072 -
obs--93.71 %
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)
14.682-1.2673-0.59524.79540.9327-0.0258-0.15850.0654-0.4283-0.02940.14450.00280.18570.10280.0140.13290.019-0.00170.06040.00350.141113.6308-1.53493.1046
27.83461.4440.414610.9453.4272.4774-0.3484-1.2066-0.0670.52290.32440.19880.27450.19460.02390.22730.07410.02180.2690.0642-0.002610.90082.985915.3161
35.6571-0.40130.25913.5725-0.00781.1968-0.08520.514-0.1053-0.16330.1490.29840.25070.0166-0.06390.0995-0.042-0.02930.09670.02390.11448.89622.31990.6515
47.1015-1.7679-1.19117.41140.3860.94480.02430.64360.8709-0.49720.20350.5227-0.0866-0.0547-0.22780.023-0.0399-0.07230.07460.14410.20445.560411.6490.5354
59.04283.31710.59423.24011.75575.5595-0.0271-0.74491.68650.46910.3011.0836-0.1231-0.0682-0.27390.09780.11470.14110.183-0.04780.6001-0.397815.388911.8884
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 42
2X-RAY DIFFRACTION2A43 - 65
3X-RAY DIFFRACTION3A66 - 99
4X-RAY DIFFRACTION4A100 - 118
5X-RAY DIFFRACTION5A119 - 135

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