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- PDB-4l0k: Crystal structure of a type II restriction endonuclease -

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Basic information

Entry
Database: PDB / ID: 4l0k
TitleCrystal structure of a type II restriction endonuclease
ComponentsDraIII
KeywordsHYDROLASE / DraIII / restriction endonuclease / REases / star activity
Function / homology: / DraIII / DraIII
Function and homology information
Biological speciesDeinococcus radiophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.328 Å
AuthorsZhuo, W. / Ge, J. / Yang, M.
CitationJournal: Protein Cell / Year: 2014
Title: Elimination of inter-domain interactions increases the cleavage fidelity of the restriction endonuclease DraIII.
Authors: Zhuo, W. / Lai, X. / Zhang, L. / Chan, S.H. / Li, F. / Zhu, Z. / Yang, M. / Sun, D.
History
DepositionMay 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DraIII
B: DraIII
C: DraIII
D: DraIII


Theoretical massNumber of molelcules
Total (without water)103,0114
Polymers103,0114
Non-polymers00
Water6,702372
1
A: DraIII
C: DraIII


Theoretical massNumber of molelcules
Total (without water)51,5062
Polymers51,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-22 kcal/mol
Surface area22040 Å2
MethodPISA
2
B: DraIII
D: DraIII


Theoretical massNumber of molelcules
Total (without water)51,5062
Polymers51,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-21 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.397, 119.063, 82.111
Angle α, β, γ (deg.)90.00, 92.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DraIII


Mass: 25752.854 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A067XG67*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O
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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% 2-propanol, 0.1M Tris pH 8.0, 5% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. all: 48056 / Num. obs: 47240 / % possible obs: 98.3 % / Rsym value: 0.047
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.33-2.41195.5
2.41-2.51198.1
2.51-2.62198.7
2.62-2.76198.8
2.76-2.94198.9
2.94-3.16199

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.328→35.724 Å / SU ML: 0.33 / σ(F): 1.37 / Phase error: 26.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2432 2389 5.06 %
Rwork0.1919 --
obs0.1945 47213 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.328→35.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6531 0 0 372 6903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116692
X-RAY DIFFRACTIONf_angle_d1.2569016
X-RAY DIFFRACTIONf_dihedral_angle_d17.3262468
X-RAY DIFFRACTIONf_chiral_restr0.0841022
X-RAY DIFFRACTIONf_plane_restr0.0051136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3277-2.37520.31741420.24422471X-RAY DIFFRACTION94
2.3752-2.42680.33271450.23342638X-RAY DIFFRACTION98
2.4268-2.48330.31951280.23292601X-RAY DIFFRACTION98
2.4833-2.54540.32051500.22322640X-RAY DIFFRACTION98
2.5454-2.61420.29341550.21732591X-RAY DIFFRACTION99
2.6142-2.69110.28591400.21992620X-RAY DIFFRACTION99
2.6911-2.77790.31141520.22462677X-RAY DIFFRACTION99
2.7779-2.87710.27261330.2092651X-RAY DIFFRACTION99
2.8771-2.99230.27651250.20412650X-RAY DIFFRACTION99
2.9923-3.12840.25341350.20582654X-RAY DIFFRACTION99
3.1284-3.29320.29671540.21012672X-RAY DIFFRACTION99
3.2932-3.49940.23081620.19122645X-RAY DIFFRACTION99
3.4994-3.76930.23831170.17632672X-RAY DIFFRACTION99
3.7693-4.14810.22941290.16992689X-RAY DIFFRACTION99
4.1481-4.74710.19711490.1522634X-RAY DIFFRACTION99
4.7471-5.97630.17961340.18292672X-RAY DIFFRACTION98
5.9763-35.72820.21271390.19152647X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -13.3695 Å / Origin y: -12.7761 Å / Origin z: -46.1502 Å
111213212223313233
T0.0834 Å2-0.0088 Å2-0.0008 Å2-0.0674 Å2-0.0022 Å2--0.0695 Å2
L0.1479 °2-0.0081 °2-0.0077 °2-0.0602 °2-0.0733 °2--0.1179 °2
S0.0503 Å °-0.0329 Å °-0.0264 Å °-0.0115 Å °-0.0128 Å °0.0115 Å °-0.0155 Å °0.0208 Å °0.007 Å °
Refinement TLS groupSelection details: all

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