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

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Basic information

Entry
Database: PDB / ID: 4rdm
TitleCrystal structure of R.NgoAVII restriction endonuclease B3 domain with cognate DNA
Components
  • DNA (5'-D(*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*G)-3)'
  • Restriction endonuclease R.NgoVII
KeywordsHYDROLASE/DNA / restriction endonuclease / B3 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 / 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 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Restriction endonuclease R.NgoVII
B: Restriction endonuclease R.NgoVII
C: DNA (5'-D(*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*G)-3)'
E: DNA (5'-D(*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*G)-3)'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7587
Polymers59,6626
Non-polymers961
Water95553
1
A: Restriction endonuclease R.NgoVII
C: DNA (5'-D(*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*G)-3)'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9274
Polymers29,8313
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-33 kcal/mol
Surface area12290 Å2
MethodPISA
2
B: Restriction endonuclease R.NgoVII
E: DNA (5'-D(*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*G)-3)'


Theoretical massNumber of molelcules
Total (without water)29,8313
Polymers29,8313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-22 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.307, 95.464, 97.817
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: NGK_0521, 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*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3)'


Mass: 4538.962 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*G)-3)'


Mass: 4625.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Crystallization buffer was 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 25, 2013
RadiationMonochromator: VARIMAX-HF MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→38.704 Å / Num. all: 16907 / Num. obs: 16907 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 40.54 Å2 / Rsym value: 0.117 / Net I/σ(I): 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.7-2.856.90.6571.11673124250.657100
2.85-3.026.90.4411.61577522970.441100
3.02-3.236.90.2452.91475121400.245100
3.23-3.496.90.1295.41402320350.129100
3.49-3.826.90.1046.91275518600.104100
3.82-4.276.80.0789.11171917110.078100
4.27-4.936.80.06810.11023315050.068100
4.93-6.046.70.06510.7872012990.065100
6.04-8.546.50.05412.8665310220.054100
8.54-38.7045.80.03212.935716130.03298.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation38.7 Å4 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREP11.0.02phasing
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.15data extraction
StructureStudiodata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→38.704 Å / SU ML: 0.38 / σ(F): 0.87 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 3071 9.8 %RANDOM
Rwork0.2179 ---
all0.2218 16907 --
obs0.2218 16809 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.97 Å2 / Biso mean: 36.81 Å2 / Biso min: 12.39 Å2
Refinement stepCycle: LAST / Resolution: 2.7→38.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2627 1200 5 53 3885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044038
X-RAY DIFFRACTIONf_angle_d0.6475713
X-RAY DIFFRACTIONf_chiral_restr0.035618
X-RAY DIFFRACTIONf_plane_restr0.003536
X-RAY DIFFRACTIONf_dihedral_angle_d23.4161551
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7001-2.74230.35211170.326313211438100
2.7423-2.78720.34491570.315112851442100
2.7872-2.83520.29291370.312112681405100
2.8352-2.88680.36941690.315512591428100
2.8868-2.94230.30731340.28911273140799
2.9423-3.00230.31481130.281413451458100
3.0023-3.06760.35551440.265712681412100
3.0676-3.13890.34841500.290612541404100
3.1389-3.21740.2971560.25081270142699
3.2174-3.30430.28451320.24991278141099
3.3043-3.40150.28451510.23031266141799
3.4015-3.51120.28281430.221313011444100
3.5112-3.63660.2251270.210512701397100
3.6366-3.78210.2421480.202912821430100
3.7821-3.95410.21961260.205113381464100
3.9541-4.16230.22971220.178512841406100
4.1623-4.42280.20141600.169912641424100
4.4228-4.76370.23391370.173512981435100
4.7637-5.2420.2031380.181912971435100
5.242-5.99810.24561270.176912911418100
5.9981-7.54780.24041440.205413011445100
7.5478-38.70770.21621390.18681268140799

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