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- PDB-4f7x: Crystal structure of Staphylococcal nuclease variant Delta+PHS I9... -

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Basic information

Entry
Database: PDB / ID: 4f7x
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS I92A/L25A at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant / pdtp / cavity / pressure
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: 1.7 Å
AuthorsCaro, J.A. / Clark, I. / Schlessman, J.L. / Heroux, A. / Garcia-Moreno E., B.
CitationJournal: To be Published
Title: Pressure effects in proteins
Authors: Caro, J.A. / Schlessman, J.L. / Garcia-Moreno E., B.
History
DepositionMay 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_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)16,5023
Polymers16,0591
Non-polymers4422
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.119, 59.908, 38.477
Angle α, β, γ (deg.)90.000, 95.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16059.303 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: L25A,G50F,V51N,I92A,P117G,H124L,S128A,del(44-49)
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / 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.: 123 / 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: 44.71 %
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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2012
RadiationMonochromator: Si(111) / Protocol: 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: 15561 / Num. obs: 15561 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.071 / Χ2: 2.338 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.7-1.735.50.16710.37831.04499.9
1.73-1.7660.1567621.232100
1.76-1.796.10.147661.23100
1.79-1.835.70.1328071.323100
1.83-1.876.30.1297491.485100
1.87-1.916.30.1237861.503100
1.91-1.966.30.1127711.762100
1.96-2.025.80.1097661.96399.5
2.02-2.076.30.0997851.984100
2.07-2.146.30.0997622.216100
2.14-2.2260.0867892.32199.6
2.22-2.316.50.0917662.478100
2.31-2.416.30.0847822.533100
2.41-2.5460.087692.71399.4
2.54-2.76.40.0767712.854100
2.7-2.9160.0747763.06199.5
2.91-3.26.30.0697963.43699.9
3.2-3.665.70.0637653.76499.6
3.66-4.615.80.067993.81199.8
4.61-505.70.068113.98599.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.33 Å
Translation2.5 Å38.33 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BDC

3bdc


Resolution: 1.7→38.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.2139 / WRfactor Rwork: 0.1776 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8843 / SU B: 3.037 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0994 / SU Rfree: 0.0984 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1973 776 5 %RANDOM
Rwork0.1628 ---
all0.1646 15543 --
obs0.1646 15543 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.57 Å2 / Biso mean: 24.1256 Å2 / Biso min: 11.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20.71 Å2
2---1.4 Å20 Å2
3---2.72 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1027 0 26 123 1176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021131
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.9991536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4135145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66125.29451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44215223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.43155
X-RAY DIFFRACTIONr_chiral_restr0.1390.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021829
LS refinement shellResolution: 1.7→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 57 -
Rwork0.186 1019 -
all-1076 -
obs-1076 94.89 %
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)
12.245-1.1259-0.47172.72610.51380.403-0.0084-0.0454-0.234-0.07110.01730.03010.05820.0501-0.00890.08330.022-0.00330.04810.01130.114814.3918-3.98182.2952
22.6274-0.2548-0.18792.45180.24391.7366-0.0635-0.2505-0.03770.20470.02850.11210.06380.05740.0350.10040.01060.00570.11790.01830.107510.11183.02818.891
32.8338-0.2925-0.35672.46890.01380.482-0.0701-0.0228-0.00430.04560.06410.1670.0536-0.0310.0060.0622-0.0027-0.01290.06520.01040.09578.59215.31173.8142
45.6682-1.3937-2.25062.25341.4715.89220.0960.2230.1899-0.2387-0.02520.2292-0.23250.0758-0.07090.06240.0049-0.02620.06220.02740.12642.363912.0097-0.9518
516.07610.59482.90434.8928-0.55857.4931-0.1329-0.64110.70710.55360.14820.5116-0.3442-0.3862-0.01530.15260.080.08450.1465-0.05920.1549-0.562315.522815.4538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 35
2X-RAY DIFFRACTION2A36 - 80
3X-RAY DIFFRACTION3A81 - 113
4X-RAY DIFFRACTION4A114 - 130
5X-RAY DIFFRACTION5A131 - 141

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