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- PDB-3bvq: Crystal Structure of Apo NotI Restriction Endonuclease -

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Basic information

Entry
Database: PDB / ID: 3bvq
TitleCrystal Structure of Apo NotI Restriction Endonuclease
ComponentsNotI restriction endonuclease
KeywordsHYDROLASE / Restriction enzyme fold / PD-(D/E)-XK / Restriction endonuclease / rare-cutting / Fe-Cys4 motif / iron-sulfur protein
Function / homologyendonuclease activity / identical protein binding / metal ion binding / : / NotI restriction endonuclease
Function and homology information
Biological speciesNocardia otitidiscaviarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsLambert, A.R. / Sussman, D. / Shen, B. / Stoddard, B.L.
CitationJournal: Structure / Year: 2008
Title: Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding.
Authors: Lambert, A.R. / Sussman, D. / Shen, B. / Maunus, R. / Nix, J. / Samuelson, J. / Xu, S.Y. / Stoddard, B.L.
History
DepositionJan 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NotI restriction endonuclease
B: NotI restriction endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8106
Polymers85,5072
Non-polymers3044
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.893, 74.893, 274.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ALA / Refine code: 4

Dom-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PROAA12 - 36412 - 364
2THRBB12 - 36612 - 366

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Components

#1: Protein NotI restriction endonuclease


Mass: 42753.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia otitidiscaviarum (bacteria) / Gene: notIR / Production host: Escherichia coli (E. coli) / References: UniProt: Q2I6W2
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 2.25 Å3/Da / Density % sol: 45.27 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9804, 0.9805, 0.9744, 1.0048
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98041
20.98051
30.97441
41.00481
ReflectionResolution: 2.8→50 Å / Num. obs: 20201 / % possible obs: 99.6 % / Redundancy: 26 % / Rmerge(I) obs: 0.109 / Χ2: 0.984 / Net I/σ(I): 11.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 21 % / Rmerge(I) obs: 0.317 / Num. unique all: 1907 / Χ2: 0.952 / % possible all: 97.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
SHARPphasing
RefinementResolution: 2.8→45.83 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.841 / SU B: 54.807 / SU ML: 0.486 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.497 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.335 1028 5.1 %RANDOM
Rwork0.262 ---
obs0.266 20107 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.375 Å2
Baniso -1Baniso -2Baniso -3
1--5.6 Å20 Å20 Å2
2---5.6 Å20 Å2
3---11.2 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5148 0 12 0 5160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225303
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.9417252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0545689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04523.657216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77915717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2731527
X-RAY DIFFRACTIONr_chiral_restr0.0730.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024117
X-RAY DIFFRACTIONr_nbd_refined0.1970.22398
X-RAY DIFFRACTIONr_nbtor_refined0.30.23615
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.26
X-RAY DIFFRACTIONr_mcbond_it0.3061.53515
X-RAY DIFFRACTIONr_mcangle_it0.50925503
X-RAY DIFFRACTIONr_scbond_it0.44532028
X-RAY DIFFRACTIONr_scangle_it0.7164.51749
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2311 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.480.5
MEDIUM THERMAL0.172
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 67 -
Rwork0.367 1332 -
all-1399 -
obs--96.15 %
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)
11.4421-0.59-0.42840.54270.14390.71640.0449-0.052-0.6187-0.0147-0.0240.14660.16730.0047-0.0209-0.1187-0.0587-0.0180.0466-0.01930.179744.878555.6957111.9606
21.33180.1173-0.51371.10830.20450.2550.0059-0.05610.08120.1510.020.06680.02730.0013-0.026-0.13920.01380.01320.04930.0125-0.070527.410280.3579124.6286
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 36412 - 364
2X-RAY DIFFRACTION2BB12 - 36612 - 366

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