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- PDB-1ouo: Crystal structure of the periplasmic endonuclease Vvn -

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Basic information

Entry
Database: PDB / ID: 1ouo
TitleCrystal structure of the periplasmic endonuclease Vvn
ComponentsNuclease
KeywordsHYDROLASE / Non-specific endonuclease / beta-beta-alpha-metal motif
Function / homologyEndonuclease I / Endonuclease I / deoxyribonuclease I / deoxyribonuclease I activity / His-Me finger superfamily / endonuclease activity / metal ion binding / Endonuclease I / Endonuclease I
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsYuan, H.S. / Li, C.L.
CitationJournal: Embo J. / Year: 2003
Title: DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site.
Authors: Li, C.-L. / Hor, L.-I. / Chang, Z.-F. / Tsai, L.-C. / Yang, W.-Z. / Yuan, H.S.
History
DepositionMar 25, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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

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Assembly

Deposited unit
A: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7202
Polymers24,6961
Non-polymers241
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.115, 40.099, 50.631
Angle α, β, γ (deg.)90.00, 90.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nuclease / VVN Nuclease


Mass: 24695.891 Da / Num. of mol.: 1 / Fragment: residue 19-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q8DCA6, UniProt: Q7MHK3*PLUS, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 1.79 Å3/Da / Density % sol: 30.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000, ammonium acetate, magnesium acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %PEG80001reservoir
20.2 Mammonium acetate1reservoir
30.01 Mmagnesium acetate1reservoir
40.05 Msodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.9795, 0.9796, 0.9600
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 16, 2001
RadiationMonochromator: SI 111 + GE 220 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97961
30.961
ReflectionResolution: 2.3→40 Å / Num. all: 9512 / Num. obs: 9127 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.822 % / Biso Wilson estimate: 15.6 Å2 / Rsym value: 0.075 / Net I/σ(I): 24.38
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 9.57 / Rsym value: 0.146 / % possible all: 96
Reflection
*PLUS
% possible obs: 96 % / Num. measured all: 62270 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 9.6

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→26.55 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 283277.67 / 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
Rfree0.269 713 8.3 %RANDOM
Rwork0.186 ---
all-16490 --
obs-8803 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.3607 Å2 / ksol: 0.348624 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1--6.33 Å20 Å24.57 Å2
2---3.15 Å20 Å2
3---9.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.3→26.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 1 194 1913
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 133 9.4 %
Rwork0.185 1275 -
obs-2424 95.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 40 Å / Num. reflection obs: 8072 / Num. reflection Rfree: 731
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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