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

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Basic information

Entry
Database: PDB / ID: 4dgz
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS I92A/L125A 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: 1.47 Å
AuthorsCaro, J.A. / Nam, S.P. / 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
DepositionJan 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 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_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: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5023
Polymers16,0591
Non-polymers4422
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.068, 60.399, 38.480
Angle α, β, γ (deg.)90.000, 93.500, 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: G50F,V51N,I92A,P117G,H124L,L125A,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.: 118 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, 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: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. all: 23894 / Num. obs: 23894 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.054 / Χ2: 2.188 / Net I/σ(I): 19.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.47-1.53.40.1698.310271.15386.2
1.5-1.5240.14911041.08891.7
1.52-1.554.60.14412221.10698.5
1.55-1.585.20.13311721.19399.8
1.58-1.625.70.11812031.303100
1.62-1.666.40.10512211.307100
1.66-1.76.30.10111991.39199.9
1.7-1.746.40.09212181.43299.8
1.74-1.796.50.08211941.536100
1.79-1.856.20.07212071.636100
1.85-1.926.50.06812181.826100
1.92-26.20.0612021.99100
2-2.096.50.05912332.33499.9
2.09-2.26.40.05712002.542100
2.2-2.336.30.05411942.73499.8
2.33-2.516.30.05212232.89399.8
2.51-2.776.60.05112103.11899.8
2.77-3.176.10.0512203.52699.5
3.17-3.9960.0512113.93298.3
3.99-505.70.05312164.24397.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.41 Å
Translation2.5 Å32.41 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.2.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BDC

3bdc


Resolution: 1.47→32.41 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2311 / WRfactor Rwork: 0.192 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8674 / SU B: 2.33 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0723 / SU Rfree: 0.0778 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.072 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 2397 10.1 %RANDOM
Rwork0.1736 ---
all0.1773 23838 --
obs0.1773 23838 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.32 Å2 / Biso mean: 24.6043 Å2 / Biso min: 12.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å20.38 Å2
2---1.34 Å20 Å2
3---2.8 Å2
Refinement stepCycle: LAST / Resolution: 1.47→32.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1027 0 26 118 1171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221135
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.9981540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3865147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2332550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81615227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.263155
X-RAY DIFFRACTIONr_chiral_restr0.1260.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021831
X-RAY DIFFRACTIONr_mcbond_it1.3821.5668
X-RAY DIFFRACTIONr_mcangle_it2.09121078
X-RAY DIFFRACTIONr_scbond_it3.2073467
X-RAY DIFFRACTIONr_scangle_it4.6694.5452
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 162 -
Rwork0.238 1387 -
all-1549 -
obs-1449 87.42 %
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)
11.6089-0.6913-0.27462.58180.33170.475-0.0180.0161-0.12830.03440.0469-0.06080.08850.0444-0.02890.0753-0.00010.00870.07280.01030.08613.6648-1.68272.9685
23.51620.97060.48255.5961.84873.09140.0078-0.3960.00080.4199-0.0263-0.06340.0570.02890.01850.12320.03460.00840.14540.03530.060710.87953.125415.299
32.74950.55450.18662.116-0.02881.0223-0.03610.2264-0.0185-0.11760.04720.05150.0281-0.0218-0.01110.08150.01150.00230.0671-0.00790.079610.45811.1663-1.2349
43.5411-0.12330.07552.67220.37630.8043-0.01660.11310.1192-0.07460.01250.0699-0.0428-0.06040.00410.06210.0051-0.00150.05290.00430.09463.950310.57942.599
54.98121.01271.86613.29461.3367.6703-0.0952-0.50370.40860.37390.02640.1609-0.2922-0.18460.06880.11540.0350.02230.0935-0.02670.1459-0.92715.794913.5791
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 42
2X-RAY DIFFRACTION2A43 - 71
3X-RAY DIFFRACTION3A72 - 98
4X-RAY DIFFRACTION4A99 - 127
5X-RAY DIFFRACTION5A128 - 141

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