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- PDB-3odh: Structure of OkrAI/DNA complex -

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Basic information

Entry
Database: PDB / ID: 3odh
TitleStructure of OkrAI/DNA complex
Components
  • DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')
  • OkrAI endonuclease
KeywordsHYDROLASE/DNA / alpha and beta proteins (a/b) / restriction endonuclease-like / phosphodiesterase / HYDROLASE-DNA complex
Function / homologyRestriction Endonuclease - #20 / Restriction Endonuclease / 3-Layer(aba) Sandwich / Alpha Beta / DNA / DNA (> 10)
Function and homology information
Biological speciesOceanobacter kriegii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVanamee, E.S. / Aggarwal, A.K.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI.
Authors: Vanamee, E.S. / Viadiu, H. / Chan, S.H. / Ummat, A. / Hartline, A.M. / Xu, S.Y. / Aggarwal, A.K.
History
DepositionAug 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.3Feb 21, 2024Group: 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_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_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.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: OkrAI endonuclease
B: OkrAI endonuclease
E: OkrAI endonuclease
F: OkrAI endonuclease
C: DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')
D: DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')
G: DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')
H: DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,38014
Polymers102,1408
Non-polymers2406
Water12,791710
1
A: OkrAI endonuclease
B: OkrAI endonuclease
C: DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')
D: DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1907
Polymers51,0704
Non-polymers1203
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-74 kcal/mol
Surface area16890 Å2
MethodPISA
2
E: OkrAI endonuclease
F: OkrAI endonuclease
G: DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')
H: DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1907
Polymers51,0704
Non-polymers1203
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-73 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.982, 83.075, 119.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
OkrAI endonuclease


Mass: 21873.535 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oceanobacter kriegii (bacteria) / Strain: NEB strain collection / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
#2: DNA chain
DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')


Mass: 3661.416 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 710 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 15-17% PEG 8000, 0.2 M calcium acetate, 0.1 M sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2calcium acetate11
3sodium cacodylate11
4PEG 800012
5calcium acetate12
6sodium cacodylate12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 30786

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
CNSrefinement
DENZOdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.899 / SU B: 14.766 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23374 1624 5 %RANDOM
Rwork0.15533 ---
obs0.15934 30786 88.83 %-
all-32438 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.335 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6007 972 6 710 7695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227221
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8712.1339974
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2955770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95423.87261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.808151079
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1591544
X-RAY DIFFRACTIONr_chiral_restr0.110.21107
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215112
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_it0.8351.53845
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50226200
X-RAY DIFFRACTIONr_scbond_it2.25933376
X-RAY DIFFRACTIONr_scangle_it3.2974.53774
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 92 -
Rwork0.209 2069 -
obs--82.42 %
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)
10.36270.09320.07230.3547-0.02560.4372-0.00670.0428-0.0017-0.02530.01120.01290.05620.0099-0.00440.0199-0.0003-0.00460.02780.00660.003712.744-11.24047.3144
20.55970.1759-0.02980.41590.11290.17590.02150.02860.1430.0415-0.01020.04790.02150.01-0.01140.0128-0.00460.00770.00870.00550.05138.864914.037519.4531
30.20230.0621-0.02720.3770.00650.2083-0.00580.0150.0098-0.06010.00830.0183-0.01490.0035-0.00250.032-0.0016-0.01030.02880.00110.005632.381746.520720.1438
40.2256-0.0573-0.04190.35080.02310.15190.0089-0.02590.03250.014400.01840.00210.0054-0.00890.0176-0.00380.00320.0351-0.01290.015228.516449.664548.1423
50.79360.14490.20060.29840.02370.0526-0.00670.055-0.05650.08310.01460.0263-0.00650.0112-0.00790.0303-0.01330.00990.04810.00250.020410.8768-4.138123.2535
60.80190.29850.64330.15060.23630.5551-0.0358-0.01420.03260.0298-0.0106-0.01450.0053-0.02050.04640.0675-0.0026-0.00730.0296-0.00270.037511.7913-3.182323.3393
71.1322-0.0459-0.12980.3172-0.01470.0167-0.00640.10270.0089-0.0030.01150.010.0026-0.0086-0.00510.02340.00880.00460.0522-0.00990.020131.062137.460335.1391
80.5153-0.42310.22890.3895-0.10870.3291-0.0633-0.0174-0.00790.02690.02280.0238-0.0285-0.01850.04050.0387-0.0103-0.00190.0542-0.00750.011731.013137.810935.9679
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 194
2X-RAY DIFFRACTION2B1 - 194
3X-RAY DIFFRACTION3E1 - 194
4X-RAY DIFFRACTION4F1 - 194
5X-RAY DIFFRACTION5C1 - 12
6X-RAY DIFFRACTION6D1 - 12
7X-RAY DIFFRACTION7G1 - 12
8X-RAY DIFFRACTION8H1 - 12

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