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- PDB-3t13: Crystal structure of Staphylococcal nuclease variant Delta+PHS A6... -

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Basic information

Entry
Database: PDB / ID: 3t13
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS A69G at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant
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
PHOSPHATE ION / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsDoctrow, B.M. / Schlessman, J.L. / Garcia-Moreno E., B. / Heroux, A.
CitationJournal: To be Published
Title: Crystal structure of Staphylococcal nuclease variant Delta+PHS A69G at cryogenic temperature
Authors: Doctrow, B.M. / Schlessman, J.L. / Garcia-Moreno E., B.
History
DepositionJul 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
B: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,09711
Polymers32,2592
Non-polymers8389
Water4,792266
1
A: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5966
Polymers16,1291
Non-polymers4665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5015
Polymers16,1291
Non-polymers3714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.595, 63.755, 49.874
Angle α, β, γ (deg.)90.00, 91.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thermonuclease / TNase / Micrococcal nuclease / Staphylococcal nuclease


Mass: 16129.438 Da / Num. of mol.: 2 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: G50F/V51N/A69G/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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00644, micrococcal nuclease
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 41% MPD, 25 mM potassium phosphate, pH 7.0, 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: Oct 19, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 27161 / Num. obs: 27161 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.085 / Χ2: 1.981 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.836.90.25913310.834199.3
1.83-1.867.40.24813680.9591100
1.86-1.97.40.22113141.078199.9
1.9-1.947.40.213811.2541100
1.94-1.987.40.18113571.4281100
1.98-2.037.40.16913531.6031100
2.03-2.087.40.15513491.782199.9
2.08-2.137.30.1413471.9641100
2.13-2.27.30.13313512.0191100
2.2-2.277.30.12113552.0811100
2.27-2.357.40.12213492.1561100
2.35-2.447.40.11313472.2871100
2.44-2.557.40.10413772.151199.9
2.55-2.697.40.09613552.332199.9
2.69-2.867.40.08913502.321100
2.86-3.087.40.08413682.549199.9
3.08-3.397.30.07613712.9031100
3.39-3.887.10.06913783.117199.9
3.88-4.8870.05913562.526199.2
4.88-507.30.05914042.228199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.16 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.85 Å
Translation2.5 Å49.85 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BDC

3bdc


Resolution: 1.8→49.85 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2059 / WRfactor Rwork: 0.1607 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8828 / SU B: 4.645 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1124 / SU Rfree: 0.1124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / 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
Rfree0.1987 1363 5 %RANDOM
Rwork0.1563 ---
all0.1585 27144 --
obs0.1585 27144 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 79.61 Å2 / Biso mean: 21.0074 Å2 / Biso min: 6.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å2-0.64 Å2
2---0.55 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 49 266 2388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222232
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9973013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg65281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43324.89898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41815446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4461510
X-RAY DIFFRACTIONr_chiral_restr0.1490.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211614
X-RAY DIFFRACTIONr_mcbond_it1.3161.51317
X-RAY DIFFRACTIONr_mcangle_it2.0222121
X-RAY DIFFRACTIONr_scbond_it3.7073915
X-RAY DIFFRACTIONr_scangle_it5.5384.5880
LS refinement shellResolution: 1.799→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 99 -
Rwork0.204 1862 -
all-1961 -
obs--98.39 %
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)
10.83990.10680.09561.2780.18760.92740.0430.0439-0.0412-0.0443-0.025-0.094-0.00180.0522-0.01810.07640.00770.00030.0481-0.01090.11679.1372.361-1.268
20.68070.4382-0.22493.3615-1.20880.81030.0287-0.0248-0.0010.17850.00530.2981-0.0118-0.1056-0.03390.0634-0.00920.00970.0329-0.01560.1088-4.709-1.9823.83
34.55960.54830.89831.9096-0.35932.1516-0.0267-0.0601-0.00740.0939-0.0644-0.0535-0.0406-0.04130.09110.11880.00750.00980.046-0.00590.09826.636-12.717-11.883
42.75340.70652.86341.33381.60157.20270.0459-0.13470.11340.0462-0.0474-0.0908-0.09680.11750.00150.0914-0.0060.00510.0415-0.0060.100625.626-8.008-12.941
55.76255.8976-3.703910.928-10.38211.68830.7285-0.14080.84281.76880.54981.5374-1.7834-1.1103-1.27830.34620.11230.27420.2549-0.02220.31279.543-16.226-18.908
66.81520.73852.5781.99960.19443.56380.1453-0.0779-0.30720.1026-0.02050.16370.2266-0.3053-0.12470.1117-0.0140.05690.05890.00560.115316.504-23.13-16.072
70.23990.7507-0.11582.5059-0.70241.2303-0.01760.0113-0.0054-0.0731-0.0064-0.10820.01530.03510.02390.11040.01460.02880.07120.01940.128629.222-8.532-17.225
80.96970.41510.30971.50.33330.9291-0.01630.04710.0056-0.1214-0.01770.05190.00790.01330.0340.08410.02080.01560.03060.00610.06724.065-13.494-23.09
93.4881.768-0.32924.84330.07812.46850.05680.1533-0.0216-0.4562-0.01630.1262-0.0377-0.0718-0.04050.14220.023-0.01770.0324-0.0080.075819.844-21.761-32.662
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 100
2X-RAY DIFFRACTION2A101 - 141
3X-RAY DIFFRACTION3B7 - 26
4X-RAY DIFFRACTION4B27 - 39
5X-RAY DIFFRACTION5B40 - 51
6X-RAY DIFFRACTION6B52 - 68
7X-RAY DIFFRACTION7B69 - 84
8X-RAY DIFFRACTION8B85 - 121
9X-RAY DIFFRACTION9B122 - 141

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