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- PDB-3p75: Crystal structure of Staphylococcal nuclease variant Delta+PHS V1... -

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Basic information

Entry
Database: PDB / ID: 3p75
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS V104D at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant / pdtp
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
THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsKhangulov, V.S. / Schlessman, J.L. / Heroux, A. / Garcia-Moreno, E.B.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Staphylococcal nuclease variant Delta+PHS V104D at cryogenic temperature
Authors: Khangulov, V.S. / Schlessman, J.L. / Garcia-Moreno, E.B.
History
DepositionOct 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
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_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_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_conn.ptnr2_label_seq_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)15,2064
Polymers14,7241
Non-polymers4823
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)31.000, 60.791, 36.838
Angle α, β, γ (deg.)90.000, 93.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thermonuclease / Micrococcal nuclease / Staphylococcal nuclease


Mass: 14723.965 Da / Num. of mol.: 1 / Mutation: G50F/V51N/V104D/P117G/H124L/S128A/Del44-49
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-THP / THYMIDINE-3',5'-DIPHOSPHATE


Type: DNA linking / Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 35% MPD(w/v), 25 mM CHES, Calcium Chloride, pdTp, pH 9.5, 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: Sep 19, 2009
Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes.
RadiationMonochromator: Double silicon(111) crystal monochromator / Protocol: 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: 15431 / Num. obs: 15431 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 40.5 Å2 / Rmerge(I) obs: 0.071 / Χ2: 5.694 / Net I/σ(I): 19.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.65-1.684.40.5345440.96768.6
1.68-1.7150.4596041.17474.3
1.71-1.745.20.4796441.49679.3
1.74-1.785.60.4317091.28488.1
1.78-1.825.90.3377811.54195
1.82-1.866.20.337741.56498
1.86-1.96.80.298112.78599
1.9-1.9670.2228092.388100
1.96-2.017.10.1988032.3299.9
2.01-2.087.20.1628184.13299.9
2.08-2.157.30.1458053.61799.9
2.15-2.247.30.1248114.47199.8
2.24-2.347.30.1138024.58499.8
2.34-2.467.30.1058015.256100
2.46-2.627.30.0858335.70899.4
2.62-2.827.30.098087.32399.8
2.82-3.1110.40.0848139.77599.8
3.11-3.5514.40.08181612.794100
3.55-4.4810.80.06482310.90999.8
4.48-506.90.0438225.2397.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.81 / 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
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 ID 3BDC with residue 104 truncated to Ala and all b-factors set to 20 A^2. Only conformation A was selected for residues with multiple conformations.

3bdc


Resolution: 1.9→30.94 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2514 / WRfactor Rwork: 0.2024 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8295 / SU B: 7.507 / SU ML: 0.112 / SU R Cruickshank DPI: 0.1619 / SU Rfree: 0.1543 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 535 5 %RANDOM
Rwork0.1866 ---
all0.1893 10782 --
obs0.1893 10782 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.72 Å2 / Biso mean: 38.78 Å2 / Biso min: 6.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.05 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.9→30.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1034 0 27 54 1115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221110
X-RAY DIFFRACTIONr_angle_refined_deg1.0232.0011502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4955137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5072550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.19315216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.88155
X-RAY DIFFRACTIONr_chiral_restr0.1020.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021815
X-RAY DIFFRACTIONr_mcbond_it1.4331.5654
X-RAY DIFFRACTIONr_mcangle_it2.0821052
X-RAY DIFFRACTIONr_scbond_it3.8713456
X-RAY DIFFRACTIONr_scangle_it5.6254.5445
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.9-1.9490.245400.26678682683099.52
1.949-2.0020.258310.25173899.865
2.002-2.060.309380.22477699.742
2.06-2.1230.296450.21871899.861
2.123-2.1930.277270.19369999.857
2.193-2.2690.225300.19668999.129
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)
13.3386-1.68430.0946.17020.58032.8642-0.00190.0823-0.2485-0.12650.1958-0.04820.27890.1167-0.19390.0991-0.0107-0.00030.1065-0.02660.092713.1171-1.99723.0153
25.99732.2050.76929.8760.89464.68230.046-0.91450.04310.79070.11710.01960.01230.1103-0.16310.21520.06420.02150.33930.01320.088511.85476.051915.8312
35.1102-0.4996-0.47983.55730.52893.9708-0.04870.3498-0.4-0.1230.19780.1670.3342-0.262-0.14910.1152-0.0323-0.03050.09330.02720.09118.41850.42591.1723
44.8109-1.0941-0.65196.595-2.48256.1023-0.17670.03570.37790.03770.320.29170.015-0.1708-0.14330.0716-0.00620.00540.07110.01040.11326.262912.4514.0081
58.3352-5.0487-6.9068.01964.199510.29690.24030.5460.338-0.6440.11330.2594-0.2776-0.1804-0.35360.0834-0.0358-0.05830.16270.08130.12351.33429.727-2.6068
68.7421.11613.01427.17013.029511.3664-0.2924-0.66620.62010.29370.14990.4131-0.5815-0.20730.14240.09190.05730.0540.1189-0.00990.1635-0.722816.364212.5254
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 41
2X-RAY DIFFRACTION2A42 - 68
3X-RAY DIFFRACTION3A69 - 103
4X-RAY DIFFRACTION4A104 - 116
5X-RAY DIFFRACTION5A117 - 126
6X-RAY DIFFRACTION6A127 - 141

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