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- PDB-2pu3: Structural adaptation of endonuclease I from the cold-adapted and... -

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Basic information

Entry
Database: PDB / ID: 2pu3
TitleStructural adaptation of endonuclease I from the cold-adapted and halophilic bacterium Vibrio salmonicida
ComponentsEndonuclease I
KeywordsHYDROLASE / cold adaptation / salt adaptation / psychrophilic enzymes / Endonuclease I
Function / homologyEndonuclease I / Endonuclease I / His-Me finger superfamily / endonuclease activity / metal ion binding / Endonuclease I
Function and homology information
Biological speciesVibrio salmonicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAltermark, B. / Helland, R. / Moe, E. / Willassen, N.P. / Smalas, A.O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structural adaptation of endonuclease I from the cold-adapted and halophilic bacterium Vibrio salmonicida.
Authors: Altermark, B. / Helland, R. / Moe, E. / Willassen, N.P. / Smalas, A.O.
History
DepositionMay 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE RESIDUE NUMBERS IN THE ENTRY FOLLOW THAT OF VIBRIO VULNIFICUS (PDB 1OUO)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6794
Polymers24,5841
Non-polymers953
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.078, 44.948, 51.746
Angle α, β, γ (deg.)90.000, 92.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endonuclease I


Mass: 24583.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio salmonicida (bacteria) / Species: Aliivibrio salmonicida / Strain: LFI1238 / Plasmid: pBAD/gIII / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q2XSL7, deoxyribonuclease I
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 30 % PEG 3350, 0.1 M Tris, 0.25 M sodium acetate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0707 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0707 Å / Relative weight: 1
ReflectionResolution: 1.5→33.923 Å / Num. all: 31040 / Num. obs: 30823 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 10.24 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 9.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 14 / Rsym value: 0.074 / % possible all: 97.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OUO

1ouo


Resolution: 1.5→33.92 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.015 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.079 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1549 5 %RANDOM
Rwork0.166 ---
all0.167 31040 --
obs0.167 30823 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.917 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.04 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 3 259 1966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221826
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.9112472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7715224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53423.7596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.95315324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5611514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021445
X-RAY DIFFRACTIONr_nbd_refined0.190.2884
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21261
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.2175
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.230
X-RAY DIFFRACTIONr_mcbond_it0.751.51105
X-RAY DIFFRACTIONr_mcangle_it1.20721742
X-RAY DIFFRACTIONr_scbond_it1.7973836
X-RAY DIFFRACTIONr_scangle_it2.8974.5730
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 128 -
Rwork0.167 2024 -
obs-2152 95.47 %

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