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- PDB-2oa9: Restriction endonuclease MvaI in the absence of DNA -

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Basic information

Entry
Database: PDB / ID: 2oa9
TitleRestriction endonuclease MvaI in the absence of DNA
ComponentsR.MvaI
KeywordsHYDROLASE / MONOMERIC ENDONUCLEASE / RESTRICTION ENZYME / MVAI
Function / homology
Function and homology information


MvaI/BcnI restriction endonuclease, recognition domain / MvaI/BcnI restriction endonuclease, catalytic domain / MvaI/BcnI restriction endonuclease / MvaI/BcnI restriction endonuclease, recognition domain / MvaI/BcnI restriction endonuclease family / PvuII Endonuclease; Chain A / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / R.MvaI
Similarity search - Component
Biological speciesKocuria varians (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsKaus-Drobek, M. / Czapinska, H. / Sokolowska, M. / Tamulaitis, G. / Szczepanowski, R.H. / Urbanke, K. / Siksnys, V. / Bochtler, M.
Citation
Journal: Nucleic Acids Res. / Year: 2007
Title: Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically.
Authors: Kaus-Drobek, M. / Czapinska, H. / Sokolowska, M. / Tamulaitis, G. / Szczepanowski, R.H. / Urbanke, C. / Siksnys, V. / Bochtler, M.
#1: Journal: To be Published
Title: Structural and Mechanistic Similarities between Restriction Endonucleases BcnI and MvaI and the DNA Repair Protein MutH.
Authors: Sokolowska, M. / Kaus-Drobek, M. / Czapinska, H. / Tamulaitis, G. / Siksnys, V. / Bochtler, M.
History
DepositionDec 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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.ptnr3_symmetry / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: R.MvaI
B: R.MvaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,28021
Polymers57,4052
Non-polymers1,87519
Water5,188288
1
A: R.MvaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,89713
Polymers28,7021
Non-polymers1,19512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: R.MvaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3828
Polymers28,7021
Non-polymers6807
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.499, 63.281, 71.892
Angle α, β, γ (deg.)90.00, 100.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein R.MvaI


Mass: 28702.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kocuria varians (bacteria) / Gene: mvaIR / Plasmid: pBAD24_R.MvaI / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q8RNV5
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 294 K / pH: 7.7
Details: 0.05 M CADMIUM SULFATE HYDRATE, 0.1 M HEPES PH 7.74, 1.2 M SODIUM ACETATE TRIHYDRATE, 0.17 M GLYCINE, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 7.70

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: May 18, 2006 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 75246 / % possible obs: 91.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.06 / Net I/σ(I): 30.8
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.23 / % possible all: 99.6

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Processing

Software
NameVersionClassification
SHELXDphasing
SHARPphasing
NCSREFmodel building
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.5→19.8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.32 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: MISSING RESOLUTION SHELL DUE TO THE PRESENCE OF AN ICE RING. IN THE CRYSTALLIZATION BUFFER CD2+, CA2+ AND NA+ IONS WERE PRESENT. ALL METAL CATIONS IN THE DENSITY WERE MODELLED AS CD2+ IONS, ...Details: MISSING RESOLUTION SHELL DUE TO THE PRESENCE OF AN ICE RING. IN THE CRYSTALLIZATION BUFFER CD2+, CA2+ AND NA+ IONS WERE PRESENT. ALL METAL CATIONS IN THE DENSITY WERE MODELLED AS CD2+ IONS, BUT IN SOME CASES THEIR IDENTITY IS UNCERTAIN. THE ACTIVE SITE IS DISTORTED AND THE METAL IONS ARE NOT BOUND TO THE ACTIVE SITE. TLS REFINEMENT USED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BOTH REFMAC AND CNS ARE USED FOR REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3629 5 %RANDOM
Rwork0.184 ---
obs0.186 72535 93.9 %-
all-72535 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å2-0.44 Å2
2--0.86 Å20 Å2
3----2.09 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3847 0 25 288 4160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213858
X-RAY DIFFRACTIONr_bond_other_d0.0070.023380
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9465205
X-RAY DIFFRACTIONr_angle_other_deg0.82137899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024315
X-RAY DIFFRACTIONr_gen_planes_other0.010.02750
X-RAY DIFFRACTIONr_nbd_refined0.2270.2716
X-RAY DIFFRACTIONr_nbd_other0.2510.23895
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.22165
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3360.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0121.52351
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.80123778
X-RAY DIFFRACTIONr_scbond_it2.6631507
X-RAY DIFFRACTIONr_scangle_it3.9794.51427
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.32 268
Rwork0.29 5727
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.292-0.80740.3920.8981-0.30181.1763-0.0772-0.05180.09850.05240.1011-0.1401-0.07920.1198-0.02390.02710.00370.01610.0086-0.01740.084352.387-3.90245.17
20.2749-0.0406-0.16990.4455-0.10551.6191-0.015-0.00310.00080.0106-0.0028-0.020400.05750.01780.0146-0.01420.01870.0261-0.01030.066145.3193.71414.049
30.97640.48781.00791.0380.99051.7437-0.0272-0.08770.0022-0.0674-0.01140.1175-0.0137-0.19160.03860.0325-0.01720.01650.0216-0.00390.081522.438-6.27428.694
40.2175-0.0453-0.22230.46430.20181.5621-0.02120.0199-0.0032-0.014-0.0153-0.00510.0149-0.04610.03650.01410.01540.01410.0215-0.00160.076530.2125.43457.804
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 651 - 68
2X-RAY DIFFRACTION1AA161 - 190164 - 193
3X-RAY DIFFRACTION1AA232 - 246235 - 249
4X-RAY DIFFRACTION2AA66 - 16069 - 163
5X-RAY DIFFRACTION2AA191 - 231194 - 234
6X-RAY DIFFRACTION3BB4 - 657 - 68
7X-RAY DIFFRACTION3BB161 - 190164 - 193
8X-RAY DIFFRACTION3BB232 - 246235 - 249
9X-RAY DIFFRACTION4BB66 - 16069 - 163
10X-RAY DIFFRACTION4BB191 - 231194 - 234

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