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- PDB-1zm8: Apo Crystal structure of Nuclease A from Anabaena sp. -

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Basic information

Entry
Database: PDB / ID: 1zm8
TitleApo Crystal structure of Nuclease A from Anabaena sp.
ComponentsNuclease
KeywordsHYDROLASE / NucA / nuclease / metal dependent
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / endonuclease activity / nucleic acid binding / periplasmic space / metal ion binding
Similarity search - Function
DNA/RNA non-specific endonuclease, active site / DNA/RNA non-specific endonucleases active site. / Non-specific endonuclease / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease ...DNA/RNA non-specific endonuclease, active site / DNA/RNA non-specific endonucleases active site. / Non-specific endonuclease / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAnabaena sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGhosh, M. / Meiss, G. / Pingoud, A. / London, R.E. / Pedersen, L.C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural Insights into the Mechanism of Nuclease A, a beta beta alpha Metal Nuclease from Anabaena.
Authors: Ghosh, M. / Meiss, G. / Pingoud, A. / London, R.E. / Pedersen, L.C.
History
DepositionMay 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9237
Polymers28,5431
Non-polymers3806
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.690, 66.682, 81.730
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 Nuclease / / Endonuclease


Mass: 28542.887 Da / Num. of mol.: 1 / Fragment: catalytic domain (residues 25-274) / Mutation: D121A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. (bacteria) / Gene: nucA / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3)
References: UniProt: P38446, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.2 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, NaCl, ZnSO4, PEG550, MnCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 21, 2004 / Details: mirrors
RadiationMonochromator: MSC-Blue mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 19775 / Num. obs: 19775 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 22.4 Å2 / Rsym value: 0.058 / Net I/σ(I): 23.8
Reflection shellHighest resolution: 1.9 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 1303 / Rsym value: 0.295 / % possible all: 64.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Serratia endonuclease pdb id code: 1G8T

1g8t


Resolution: 1.9→30.87 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 739023.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 915 4.8 %RANDOM
Rwork0.212 ---
all0.214 19791 --
obs0.212 18876 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.3197 Å2 / ksol: 0.361788 e/Å3
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1-23.26 Å20 Å20 Å2
2---8.41 Å20 Å2
3----14.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.9→30.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 14 145 1989
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it1.712
X-RAY DIFFRACTIONc_scangle_it2.352.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 102 4.6 %
Rwork0.305 2106 -
obs--65 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4so4.parso4.top

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