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- PDB-4rd5: Crystal structure of R.NgoAVII restriction endonuclease B3 domain... -

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Basic information

Entry
Database: PDB / ID: 4rd5
TitleCrystal structure of R.NgoAVII restriction endonuclease B3 domain with cognate DNA
Components
  • DNA (5'-D(*CP*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*AP*TP*TP*GP*CP*CP*GP*CP*TP*TP*AP*GP*G)-3')
  • Restriction endonuclease R.NgoVII
KeywordsHYDROLASE/DNA / restriction endonuclease / B3 DNA binding domain / protein-DNA complex / HYDROLASE-DNA complex
Function / homologyRestriction endonuclease, type II, NgoFVII / : / NgoFVII restriction endonuclease N-terminal PLD domain / NgoFVII C-terminal B3-like DNA-binding domain / endonuclease activity / DNA / DNA (> 10) / Restriction endonuclease NgoFVII
Function and homology information
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsTamulaitiene, G. / Silanskas, A. / Grazulis, S. / Zaremba, M. / Siksnys, V.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII.
Authors: Tamulaitiene, G. / Silanskas, A. / Grazulis, S. / Zaremba, M. / Siksnys, V.
History
DepositionSep 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Restriction endonuclease R.NgoVII
B: Restriction endonuclease R.NgoVII
C: DNA (5'-D(*CP*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3')
D: DNA (5'-D(*GP*GP*GP*AP*TP*TP*GP*CP*CP*GP*CP*TP*TP*AP*GP*G)-3')
E: DNA (5'-D(*CP*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3')
F: DNA (5'-D(*GP*GP*GP*AP*TP*TP*GP*CP*CP*GP*CP*TP*TP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)60,9296
Polymers60,9296
Non-polymers00
Water1,54986
1
A: Restriction endonuclease R.NgoVII
C: DNA (5'-D(*CP*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3')
D: DNA (5'-D(*GP*GP*GP*AP*TP*TP*GP*CP*CP*GP*CP*TP*TP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)30,4643
Polymers30,4643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-21 kcal/mol
Surface area12210 Å2
MethodPISA
2
B: Restriction endonuclease R.NgoVII
E: DNA (5'-D(*CP*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3')
F: DNA (5'-D(*GP*GP*GP*AP*TP*TP*GP*CP*CP*GP*CP*TP*TP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)30,4643
Polymers30,4643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-22 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.414, 88.414, 152.437
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-455-

HOH

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Components

#1: Protein Restriction endonuclease R.NgoVII


Mass: 20666.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: ATCC 700825 / FA 1090 / Gene: NGO0364 / Plasmid: pLATE31 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q5F9M9, type II site-specific deoxyribonuclease
#2: DNA chain DNA (5'-D(*CP*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3')


Mass: 4828.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct
#3: DNA chain DNA (5'-D(*GP*GP*GP*AP*TP*TP*GP*CP*CP*GP*CP*TP*TP*AP*GP*G)-3')


Mass: 4970.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystallization buffer was 0.1 M MES-imidazole pH 6.5, 12.5% w/v PEG1000, 12.5% w/v PEG3350, 12.5% MPD, 0.02 M of each Glu, Ala, Gly, Lys, Ser, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 21, 2013
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→152.437 Å / Num. all: 17327 / Num. obs: 17327 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.1 % / Biso Wilson estimate: 33.45 Å2 / Rsym value: 0.097 / Net I/σ(I): 32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.7-2.8518.60.3451.94599424790.345100
2.85-3.0220.30.2662.44706423160.266100
3.02-3.2320.10.1743.64429422000.174100
3.23-3.4919.40.1125.64017620710.112100
3.49-3.8218.90.0973604519110.09100
3.82-4.27200.0748.53467317370.074100
4.27-4.9318.90.0659.42969115680.065100
4.93-6.0417.80.069.82352113220.06100
6.04-8.5418.20.0598.51944610670.059100
8.54-152.43714.80.0566.797336560.05699.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å76.48 Å
Translation4 Å76.48 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREP6phasing
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.15data extraction
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→48.337 Å / SU ML: 0.33 / σ(F): 1.67 / Phase error: 24.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 3242 10.23 %RANDOM
Rwork0.2138 ---
all0.2175 17327 --
obs0.2175 17265 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.36 Å2 / Biso mean: 36.24 Å2 / Biso min: 5.23 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 1224 0 86 3793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063923
X-RAY DIFFRACTIONf_angle_d0.7945566
X-RAY DIFFRACTIONf_chiral_restr0.041606
X-RAY DIFFRACTIONf_plane_restr0.005512
X-RAY DIFFRACTIONf_dihedral_angle_d24.051496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.74030.25341580.249512331391100
2.7403-2.78310.30481330.262412511384100
2.7831-2.82880.34661640.262711931357100
2.8288-2.87750.32051400.248812261366100
2.8775-2.92980.23781580.264412431401100
2.9298-2.98620.27791260.249312551381100
2.9862-3.04710.32741300.260412611391100
3.0471-3.11340.32721600.249211851345100
3.1134-3.18580.27881290.235612841413100
3.1858-3.26540.2131250.229412301355100
3.2654-3.35370.24121390.201512231362100
3.3537-3.45240.25861500.21412341384100
3.4524-3.56380.21861350.20112551390100
3.5638-3.69110.31681390.208112331372100
3.6911-3.83880.2661320.201512641396100
3.8388-4.01350.2041220.200212671389100
4.0135-4.22490.23641590.18411971356100
4.2249-4.48950.21311300.17812531383100
4.4895-4.83580.21071440.193212231367100
4.8358-5.32190.2211520.186312321384100
5.3219-6.09070.23441480.206312251373100
6.0907-7.66870.25011300.24612581388100
7.6687-48.34510.22621390.19461230136999

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