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- PDB-1oup: Crystal structure of the periplasmic endonuclease Vvn complexed w... -

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Basic information

Entry
Database: PDB / ID: 1oup
TitleCrystal structure of the periplasmic endonuclease Vvn complexed with octamer double stranded DNA
Components
  • 5'-D(*GP*CP*GP*AP*TP*C)-3'
  • 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
  • 5'-D(P*GP*C)-3'
  • Nuclease
KeywordsHYDROLASE/DNA / Non-specific endonuclease / beta-beta-alpha metal motif / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


deoxyribonuclease I / deoxyribonuclease I activity / endonuclease activity / metal ion binding
Similarity search - Function
Endonuclease I / Endonuclease I / His-Me finger superfamily
Similarity search - Domain/homology
DNA / Endonuclease I / Endonuclease I
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.3Oct 11, 2017Group: Refinement description / Category: refine_ls_shell
Item: _refine_ls_shell.number_reflns_obs / _refine_ls_shell.percent_reflns_obs
Revision 1.4Nov 10, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
D: 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
E: 5'-D(*GP*CP*GP*AP*TP*C)-3'
G: 5'-D(P*GP*C)-3'
F: 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
A: Nuclease
B: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2499
Polymers59,1697
Non-polymers802
Water5,909328
1
C: 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
D: 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
B: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6474
Polymers29,6073
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*GP*CP*GP*AP*TP*C)-3'
G: 5'-D(P*GP*C)-3'
F: 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
A: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6025
Polymers29,5624
Non-polymers401
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.74, 50.11, 89.61
Angle α, β, γ (deg.)90.00, 97.53, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTwo protein/DNA complexes per asymmetry uint. Chains A,E,F are enzyme/product complex. Chains B,C,D are enzyme/substrate complex

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Components

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DNA chain , 3 types, 5 molecules CDFEG

#1: DNA chain 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'


Mass: 2427.605 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*CP*GP*AP*TP*C)-3'


Mass: 1809.218 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(P*GP*C)-3'


Mass: 573.430 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AB

#4: Protein Nuclease / VVN Nuclease


Mass: 24751.709 Da / Num. of mol.: 2 / Fragment: residues 19-231 / Mutation: H80A
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

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Non-polymers , 2 types, 330 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.93 Å3/Da / Density % sol: 35.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG3350, Calcium acetate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG335011
2Calcium acetate11
3PEG335012
4Calcium acetate12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %1reservoir
20.2 Mcalcium acetate1reservoir
31
41

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.9065 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9065 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 21213 / Num. obs: 21165 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.073 / Net I/σ(I): 20.2
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 4.4 / Rsym value: 0.282 / % possible all: 100
Reflection
*PLUS
Num. measured all: 157796 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Rmerge(I) obs: 0.282

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet-Vvn

Resolution: 2.3→19.78 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1616 7.8 %RANDOM
Rwork0.191 ---
all-21279 --
obs-20729 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.7232 Å2 / ksol: 0.332758 e/Å3
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1-6.45 Å20 Å23.92 Å2
2---0.99 Å20 Å2
3----5.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 645 2 328 4425
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d1.14
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 264 8 %
Rwork0.201 3025 -
obs-953 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA-VVN.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 40 Å / Num. reflection obs: 19113 / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.14

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