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- PDB-3nk9: Crystal structure of Staphylococcal nuclease variant Delta+PHS V7... -

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Basic information

Entry
Database: PDB / ID: 3nk9
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS V74A at cryogenic temperature
ComponentsNuclease A
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: 1.65 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 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3May 30, 2012Group: Database references
Revision 1.4Sep 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: Nuclease A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5583
Polymers16,1151
Non-polymers4422
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.075, 60.435, 38.129
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nuclease A


Mass: 16115.410 Da / Num. of mol.: 1 / Mutation: G50F, V51N, V74A, P117G, H124L, S128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / 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.: 76 / 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: 44.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 8.0, 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: 1.65→50 Å / Num. all: 16836 / Num. obs: 16836 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 22.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.65-1.686.50.183196
1.68-1.716.70.176199.3
1.71-1.7470.157198.9
1.74-1.787.30.141199.3
1.78-1.827.40.117199.8
1.82-1.867.30.104199.6
1.86-1.97.40.095199.7
1.9-1.967.30.079199.6
1.96-2.017.40.075199.9
2.01-2.087.40.063199.5
2.08-2.157.30.059199.3
2.15-2.247.30.054199.5
2.24-2.347.40.052199.9
2.34-2.467.30.051100
2.46-2.627.20.051100
2.62-2.827.20.049199.9
2.82-3.117.10.0471100
3.11-3.556.80.04198.9
3.55-4.486.90.038196.4
4.48-506.80.038189.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.16 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å23.4 Å
Translation2.5 Å23.4 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, Q30A, K64A, V74A, T82A, Y113A, V114A and Y115A; all b-factors were reset to 20 A^2.

3bdc


Resolution: 1.65→30.22 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.93 / SU ML: 0.068 / SU R Cruickshank DPI: 0.1118 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 1677 10 %RANDOM
Rwork0.18132 ---
obs0.1855 15112 98.78 %-
all-16991 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.894 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å20.85 Å2
2---1.69 Å20 Å2
3---3.68 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1031 0 26 76 1133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221103
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6112.0081493
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4185138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66624.89447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41315216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.275155
X-RAY DIFFRACTIONr_chiral_restr0.1230.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021801
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_it1.3181.5654
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91521052
X-RAY DIFFRACTIONr_scbond_it3.0393449
X-RAY DIFFRACTIONr_scangle_it4.3984.5436
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 105 -
Rwork0.196 1086 -
obs--96.91 %
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)
11.6660.2396-0.54672.52751.16440.8087-0.1167-0.0654-0.22240.08640.0761-0.05230.11240.06890.04070.10620.0277-0.01510.05990.01080.089113.2229-3.84013.6761
22.8273-5.0063-1.11049.09382.2190.97060.03060.0703-0.05690.0126-0.0342-0.0640.1141-0.00230.00360.06380.01690.0330.0753-0.06180.225316.5677-2.15690.7781
33.03350.103-0.28762.59060.4311.4446-0.0808-0.5750.09990.44190.0824-0.08060.06110.1597-0.00150.1260.0307-0.01520.1568-0.00130.016511.43066.195913.8618
42.4282-0.65170.05292.53250.48720.5335-0.01210.1462-0.0093-0.0790.02530.12330.0363-0.0208-0.01320.0727-0.00910.00230.07250.01770.04637.83794.87420.896
54.5170.14921.72092.80340.54054.0352-0.222-0.51790.48170.34120.13140.4114-0.2574-0.06510.09060.07530.03590.0470.0708-0.04060.1371-0.821915.207211.0539
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 27
2X-RAY DIFFRACTION2A28 - 36
3X-RAY DIFFRACTION3A37 - 63
4X-RAY DIFFRACTION4A64 - 117
5X-RAY DIFFRACTION5A118 - 135

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