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- PDB-2xh3: extracellular nuclease -

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Basic information

Entry
Database: PDB / ID: 2xh3
Titleextracellular nuclease
ComponentsSPD1 NUCLEASE
KeywordsHYDROLASE / ENDONUCLEASE
Function / homology
Function and homology information


nucleic acid binding / hydrolase activity / metal ion binding
Similarity search - Function
Type VII secretion system protein EssD-like / DNA/RNA non-specific endonuclease / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / DNase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PYOGENES SEROTYPE M1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsKorczynska, J.E. / Turkenburg, J.P. / Taylor, E.J.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The Structural Characterization of a Prophage-Encoded Extracellular DNase from Streptococcus Pyogenes.
Authors: Korczynska, J.E. / Turkenburg, J.P. / Taylor, E.J.
History
DepositionJun 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Jan 25, 2012Group: Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: SPD1 NUCLEASE
B: SPD1 NUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8223
Polymers56,7152
Non-polymers1061
Water3,099172
1
A: SPD1 NUCLEASE


Theoretical massNumber of molelcules
Total (without water)28,3581
Polymers28,3581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SPD1 NUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4642
Polymers28,3581
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.822, 101.822, 113.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SPD1 NUCLEASE / PUTATIVE DNASE


Mass: 28357.732 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PYOGENES SEROTYPE M1 (bacteria)
Strain: GAS-SF370 / Plasmid: PET28LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIPL / References: UniProt: Q9A0M1, deoxyribonuclease I
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 145 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASN 145 TO ALA

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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: 2.57 Å3/Da / Density % sol: 52.2 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2M NA CITRATE, 0.1M BIS-TRIS PROPANE PH 8.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 5, 2010 / Details: OSMIC MULTILAYER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.5→50.9 Å / Num. obs: 18955 / % possible obs: 90.3 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.5
Reflection shellResolution: 2.48→2.61 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.5 / % possible all: 82.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0077refinement
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XGR

2xgr


Resolution: 2.49→113.55 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.897 / SU B: 6.637 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-47, 87-112 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.24414 972 5.1 %RANDOM
Rwork0.16682 ---
obs0.1706 17974 89.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.523 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2---0.32 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.49→113.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2815 0 7 172 2994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212882
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.9493928
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2835353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.06125.172145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94115455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9011514
X-RAY DIFFRACTIONr_chiral_restr0.1190.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212226
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.486→2.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 59 -
Rwork0.245 1187 -
obs--83.12 %

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