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- PDB-3nxw: Crystal structure of Staphylococcal nuclease variant Delta+PHS L1... -

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Basic information

Entry
Database: PDB / ID: 3nxw
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS L125A 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 / 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
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
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)16,5443
Polymers16,1011
Non-polymers4422
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.947, 60.640, 38.177
Angle α, β, γ (deg.)90.00, 92.54, 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
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
#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.: 54 / 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: 44.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 29% 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: 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 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 17169 / Num. obs: 17169 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.057 / Χ2: 2.283 / Net I/σ(I): 20.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.685.20.2078070.977193.9
1.68-1.715.90.1958311.069197.1
1.71-1.747.10.1688781.102199.3
1.74-1.787.30.1568221.1861100
1.78-1.827.20.1268661.3781100
1.82-1.867.30.1198561.5171100
1.86-1.97.40.1198571.6671100
1.9-1.967.50.1048701.8471100
1.96-2.017.70.1058673.1841100
2.01-2.0880.0948582.1171100
2.08-2.158.30.0948472.2351100
2.15-2.248.50.088752.371100
2.24-2.349.10.0848432.5941100
2.34-2.469.90.0818762.6671100
2.46-2.6210.40.0678672.5641100
2.62-2.8210.30.0628652.597199.9
2.82-3.1110.10.0538782.731100
3.11-3.559.70.0498613.017199.9
3.55-4.488.60.0488643.279199.2
4.48-507.70.0498813.332198.2

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Phasing

Phasing MRRfactor: 35.8 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.92 Å
Translation2.5 Å30.92 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, Q80, T82A, M98A, Y113A, V114A, Y115A, K116A, L125A, Q131A, K134A, K136A; all b-factors ...Starting model: 3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, Q30A, K64A, Q80, T82A, M98A, Y113A, V114A, Y115A, K116A, L125A, Q131A, K134A, K136A; all b-factors were reset to 20 A2.

3bdc


Resolution: 1.65→30.92 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2567 / WRfactor Rwork: 0.2059 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8558 / SU B: 3.705 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1056 / SU Rfree: 0.1116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 1701 10 %RANDOM
Rwork0.1882 ---
all0.1882 17019 --
obs0.193 16938 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.07 Å2 / Biso mean: 27.946 Å2 / Biso min: 15.28 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å20.28 Å2
2---0.08 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 26 54 1110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221116
X-RAY DIFFRACTIONr_angle_refined_deg1.6332.0021514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0445142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50925.10249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93815219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.964155
X-RAY DIFFRACTIONr_chiral_restr0.1310.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021817
X-RAY DIFFRACTIONr_mcbond_it1.2761.5660
X-RAY DIFFRACTIONr_mcangle_it1.95521065
X-RAY DIFFRACTIONr_scbond_it3.1033456
X-RAY DIFFRACTIONr_scangle_it4.4484.5442
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 112 -
Rwork0.218 1068 -
all-1180 -
obs--96.09 %
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)
12.309-0.40850.02272.57270.27670.5744-0.00650.0866-0.10790.07160.0892-0.07650.07970.1073-0.08270.06410.0239-0.00020.0930.00350.085113.8893-1.0343.9427
23.20430.6270.38356.05352.65433.6753-0.0737-0.4096-0.01710.34540.10840.06730.12240.1082-0.03470.11560.03060.01950.1190.04310.03810.05972.14215.3806
32.6764-0.43930.6282.7714-0.05250.1907-0.00960.37630.0052-0.12780.0590.09970.05380.0865-0.04950.0981-0.0091-0.03370.12160.02150.08679.65611.3405-0.0901
43.6114-1.0787-0.50314.1087-0.1483.1351-0.05930.13360.2315-0.0501-0.02560.1406-0.13130.09060.08490.0352-0.005-0.00050.080.04070.15476.49312.16294.1384
52.6957-0.74950.02633.47441.16123.1732-0.1517-0.08810.37350.13870.14250.4355-0.1875-0.06680.00920.03160.01180.01520.06110.03930.1968-0.207113.4487.3942
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 44
2X-RAY DIFFRACTION2A45 - 65
3X-RAY DIFFRACTION3A66 - 97
4X-RAY DIFFRACTION4A98 - 111
5X-RAY DIFFRACTION5A112 - 135

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