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- PDB-1h56: Structural and biochemical characterization of a new magnesium io... -

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Basic information

Entry
Database: PDB / ID: 1h56
TitleStructural and biochemical characterization of a new magnesium ion binding site near Tyr94 in the restriction endonuclease PvuII
ComponentsTYPE II RESTRICTION ENZYME PVUII
KeywordsENDONUCLEASE / TYPE II RESTRICTION ENDONUCLEASE / HYDROLASE / NUCLEASE
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / metal ion binding
Similarity search - Function
PVUII Endonuclease, subunit A / Restriction endonuclease, type II, PvuII / Restriction endonuclease, type II, PvuII superfamily / Restriction endonuclease PvuII / PvuII Endonuclease; Chain A / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Type II restriction enzyme PvuII
Similarity search - Component
Biological speciesPROTEUS VULGARIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å
AuthorsSpyrida, A. / Matzen, C. / Lanio, T. / Jeltsch, A. / Simoncsits, A. / Athanasiadis, A. / Scheuring-Vanamee, E. / Kokkinidis, M. / Pingoud, A.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Structural and Biochemical Characterization of a New Mg(2+) Binding Site Near Tyr94 in the Restriction Endonuclease PvuII.
Authors: Spyridaki, A. / Matzen, C. / Lanio, T. / Jeltsch, A. / Simoncsits, A. / Athanasiadis, A. / Scheuring-Vanamee, E. / Kokkinidis, M. / Pingoud, A.
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: Crystal Structure of PvuII Endonuclease Reveals Extensive Structural Homologies to EcoRV
Authors: Athanasiadis, A. / Vlassi, M. / Kotsifaki, D. / Tucker, P.A. / Wilson, K.S. / Kokkinidis, M.
History
DepositionMay 20, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 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 / 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_database_status.status_code_sf / _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.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.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_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: TYPE II RESTRICTION ENZYME PVUII
B: TYPE II RESTRICTION ENZYME PVUII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5284
Polymers36,4802
Non-polymers492
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.180, 105.280, 46.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein TYPE II RESTRICTION ENZYME PVUII / ENDONUCLEASE PVUII / R.PVUII


Mass: 18239.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROTEUS VULGARIS (bacteria) / Plasmid: PPVU1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HB101
References: UniProt: P23657, type II site-specific deoxyribonuclease
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growpH: 5 / Details: pH 5.00
Crystal grow
*PLUS
Method: other / Details: Athanasiadis, A., (1991) J. Mol. Biol., 222, 451.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3→8 Å / Num. obs: 8104 / % possible obs: 92.3 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.13
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 8 Å / Rmerge(I) obs: 0.13

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1PVU

1pvu


Resolution: 3→8 Å / Rfactor Rfree error: 0.009 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rwork0.15 ---
obs0.15 8104 92.3 %-
Rfree-808 10.5 %RANDOM
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2584 0 2 68 2654
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.471.5
X-RAY DIFFRACTIONc_mcangle_it11.762
X-RAY DIFFRACTIONc_scbond_it9.892
X-RAY DIFFRACTIONc_scangle_it14.392.5
LS refinement shellResolution: 3→3.18 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 148 11.8 %
Rwork0.217 1101 -
obs--93.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAM
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 8 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.264 / Rfactor Rwork: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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