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- PDB-3v20: Crystal structure of Type IIF restriction endonuclease Bse634I wi... -

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Basic information

Entry
Database: PDB / ID: 3v20
TitleCrystal structure of Type IIF restriction endonuclease Bse634I with cognate DNA
Components
  • DNA (5'-D(*TP*CP*GP*CP*AP*CP*CP*GP*GP*TP*GP*CP*G)-3')
  • Endonuclease Bse634IR
KeywordsDNA BINDING PROTEIN / HYDROLASE/DNA / RESTRICTION ENDONUCLEASE / protein-DNA complex / HYDROLASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


endonuclease activity / metal ion binding
Similarity search - Function
Restriction Endonuclease - #10 / Restriction endonuclease, type II, Cfr10I/Bse634I / Cfr10I/Bse634I restriction endonuclease / Restriction Endonuclease / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7PE / DNA / DNA (> 10) / Endonuclease Bse634IR
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.35 Å
AuthorsManakova, E.N. / Grazulis, S. / Golovenko, D. / Tamulaitiene, G.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease.
Authors: Manakova, E. / Grazulis, S. / Zaremba, M. / Tamulaitiene, G. / Golovenko, D. / Siksnys, V.
History
DepositionDec 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Mar 18, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol / struct_conn / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_scientific_name / _struct_ref_seq_dif.details
Revision 1.3Sep 13, 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_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.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_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: Endonuclease Bse634IR
B: Endonuclease Bse634IR
C: DNA (5'-D(*TP*CP*GP*CP*AP*CP*CP*GP*GP*TP*GP*CP*G)-3')
D: DNA (5'-D(*TP*CP*GP*CP*AP*CP*CP*GP*GP*TP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8898
Polymers75,4634
Non-polymers4264
Water1,910106
1
A: Endonuclease Bse634IR
C: DNA (5'-D(*TP*CP*GP*CP*AP*CP*CP*GP*GP*TP*GP*CP*G)-3')
hetero molecules

A: Endonuclease Bse634IR
C: DNA (5'-D(*TP*CP*GP*CP*AP*CP*CP*GP*GP*TP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,23410
Polymers75,4634
Non-polymers7726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area11250 Å2
ΔGint-71 kcal/mol
Surface area27410 Å2
MethodPISA
2
B: Endonuclease Bse634IR
D: DNA (5'-D(*TP*CP*GP*CP*AP*CP*CP*GP*GP*TP*GP*CP*G)-3')
hetero molecules

B: Endonuclease Bse634IR
D: DNA (5'-D(*TP*CP*GP*CP*AP*CP*CP*GP*GP*TP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5436
Polymers75,4634
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10220 Å2
ΔGint-78 kcal/mol
Surface area27280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.937, 87.387, 125.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / DNA chain , 2 types, 4 molecules ABCD

#1: Protein Endonuclease Bse634IR


Mass: 33762.758 Da / Num. of mol.: 2 / Mutation: R226A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: 1422 / Gene: bse634IR / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2267
References: UniProt: Q8RT53, type II site-specific deoxyribonuclease
#2: DNA chain DNA (5'-D(*TP*CP*GP*CP*AP*CP*CP*GP*GP*TP*GP*CP*G)-3')


Mass: 3968.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 110 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THE RESIDUES AT POSITION 110, 111, AND 130 ARE CORRECTLY IDENTIFIED AND THE ...AUTHORS STATE THAT THE RESIDUES AT POSITION 110, 111, AND 130 ARE CORRECTLY IDENTIFIED AND THE BIOCHEMICAL DATA SHOWS THAT THE PROTEIN IS ACTIVE.

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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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 293 K / pH: 5.5
Details: 100mM Na-acetate pH 4.25-5.5, 10mM CaCl2 or CaAc2, 4-8% (w/v) of PEG8000, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148
DetectorType: MAR555 / Detector: CCD / Date: Sep 25, 2007
RadiationMonochromator: SI (111), HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGT / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 2.336→55.556 Å / Num. obs: 30943 / % possible obs: 90.6 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 22.8
Reflection shellResolution: 2.34→2.46 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.332 / % possible all: 64.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
MOSFLMdata reduction
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOLREPphasing
RefinementStarting model: 1KNV

1knv


Resolution: 2.35→55.556 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.866 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 19.258 / SU ML: 0.209 / SU R Cruickshank DPI: 0.576 / Cross valid method: THROUGHOUT / ESU R: 0.561 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29343 3156 10.2 %RANDOM
Rwork0.2403 ---
obs0.2457 27769 91.58 %-
all-34081 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.628 Å2
Baniso -1Baniso -2Baniso -3
1--2.09 Å20 Å20 Å2
2--3.28 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.35→55.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4687 526 24 106 5343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225439
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1862.0887460
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3045586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42324.956226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15715921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6811524
X-RAY DIFFRACTIONr_chiral_restr0.0750.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213846
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4131.52919
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.78624760
X-RAY DIFFRACTIONr_scbond_it1.13432520
X-RAY DIFFRACTIONr_scangle_it1.8164.52700
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.346→2.407 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 164 -
Rwork0.376 1370 -
obs--61.76 %
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)
12.7469-1.3151-2.15042.49072.00416.9688-0.0746-0.42070.10130.5120.2041-0.2367-0.31020.7046-0.12950.2124-0.026-0.08240.3530.00050.105816.68757.844582.2172
21.1863-0.0609-0.38020.36280.55933.3722-0.0644-0.11810.04650.18330.0057-0.0976-0.07860.61490.05870.1783-0.0214-0.06350.33680.00650.153118.53585.093870.9686
32.44840.36441.74842.2793-0.3042.3644-0.14560.11760.33490.15510.0880.0289-0.6399-0.08540.05760.28920.01870.05450.22440.06120.14334.632915.655747.4935
41.17760.0809-0.26120.5154-0.01022.4236-0.01680.1622-0.0080.0675-0.0387-0.0821-0.08480.42210.05550.04880.0003-0.01350.24450.00010.145715.71622.230354.0958
59.6299-5.2249-2.63822.8421.470911.16120.32780.1780.3005-0.2177-0.0966-0.1858-1.54060.1535-0.23120.5995-0.03020.06130.18420.00470.10966.858916.9721-18.9037
61.1039-0.0012-1.13140.94930.96557.26380.01170.26720.1662-0.7049-0.2520.0803-1.3354-1.14070.24030.63230.3084-0.14390.5389-0.04680.1168-4.73216.9726-17.373
70.31060.38520.22511.1224-0.20212.7841-0.0336-0.08290.0924-0.1606-0.15020.024-0.51840.23590.18380.22460.0793-0.03840.398-0.03190.12784.765816.74319.7887
80.64810.05620.10951.02510.07992.1412-0.0706-0.17690.1506-0.1782-0.12560.1657-0.4205-0.2470.19620.18010.1665-0.05660.3465-0.05520.1401-3.555214.876710.9919
91.99721.523-0.57732.8477-4.800411.45790.1479-0.48710.14870.7659-0.14730.1187-1.6795-0.4749-0.00060.51050.0319-0.01870.1569-0.07280.4048-0.428717.84568.9526
102.7823-0.29270.52062.0387-0.01160.1008-0.1011-0.47570.0985-0.01810.0831-0.18650.0013-0.09070.0180.18780.0078-0.00160.1642-0.0080.14174.17350.921470.9732
1117.07051.2909-0.75440.6707-2.74312.6394-0.27010.3978-1.042-0.15310.1352-0.09220.6787-0.52630.13490.1897-0.02970.06090.0964-0.03540.1969-6.4268-14.174274.1811
122.11951.61212.20897.15673.82293.0767-0.67290.21740.129-0.73880.8385-0.7298-0.77450.4725-0.16560.2557-0.07590.06620.4739-0.06680.271714.68747.0315-2.8897
131.3713-3.2668-1.53718.26923.18042.24550.24050.2031-0.1111-0.8079-0.57560.0935-0.1385-0.2190.33510.27520.1298-0.03150.3531-0.02120.136-2.50273.3712-7.0423
145.3789-2.2926-0.69597.3795-1.182417.6504-0.2739-0.2848-0.28560.08220.49940.66620.8904-1.1306-0.22550.23540.0095-0.00640.32330.01990.1325-10.2921-11.2707-8.5278
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 50
2X-RAY DIFFRACTION2A51 - 107
3X-RAY DIFFRACTION3A108 - 145
4X-RAY DIFFRACTION4A146 - 292
5X-RAY DIFFRACTION5B5 - 35
6X-RAY DIFFRACTION6B36 - 67
7X-RAY DIFFRACTION7B68 - 154
8X-RAY DIFFRACTION8B155 - 292
9X-RAY DIFFRACTION9C1 - 4
10X-RAY DIFFRACTION10C5 - 9
11X-RAY DIFFRACTION11C10 - 13
12X-RAY DIFFRACTION12D1 - 5
13X-RAY DIFFRACTION13D6 - 9
14X-RAY DIFFRACTION14D10 - 13

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