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- PDB-4rct: Crystal structure of R-protein of NgoAVII restriction endonuclease -

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Basic information

Entry
Database: PDB / ID: 4rct
TitleCrystal structure of R-protein of NgoAVII restriction endonuclease
ComponentsRestriction endonuclease R.NgoVII
KeywordsHYDROLASE / restriction endonuclease / B3 domain / PLD nuclease
Function / homology
Function and homology information


endonuclease activity
Similarity search - Function
Restriction endonuclease, type II, NgoFVII / : / NgoFVII restriction endonuclease N-terminal PLD domain / NgoFVII C-terminal B3-like DNA-binding domain / Endonuclease Chain A / Endonuclease; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Restriction endonuclease NgoFVII
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.25 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 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Nov 27, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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


Theoretical massNumber of molelcules
Total (without water)84,4352
Polymers84,4352
Non-polymers00
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-21 kcal/mol
Surface area30040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.513, 106.799, 108.235
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: 42217.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag / Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: ATCC 700825 / FA 1090 / Gene: NGK_0521, NGO0364 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q5F9M9, type II site-specific deoxyribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Crystallization buffer was 0.1 M Sodium chloride, 0.1 M Na-BICINE pH 9.0, 20% v/v PEGMME 550, 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: Oct 24, 2012
RadiationMonochromator: VARIMAX-HF MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 11.5 % / Number: 254521 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / D res high: 2.7 Å / D res low: 28.075 Å / Num. obs: 22169 / % possible obs: 99
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
8.8528.0810.0290.0299.7
6.268.8510.040.0411.3
5.116.2610.0450.04511.7
4.435.1110.0450.04511.9
3.964.4310.0590.05912
3.613.9610.1190.11911.7
3.353.6110.1590.15912
3.133.3510.1990.19912
2.953.1310.2740.27411.8
2.82.9510.3610.3619.9
ReflectionResolution: 1.685→29.735 Å / Num. all: 42289 / Num. obs: 42289 / % possible obs: 99.9 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 1.8 / Redundancy: 7.6 % / Biso Wilson estimate: 27.02 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 23.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.25-2.377.60.3921.84632961190.392100
2.37-2.527.70.2822.64404857510.282100
2.52-2.697.70.2063.64188954360.206100
2.69-2.97.70.14653916250770.146100
2.9-3.187.70.10373602646620.103100
3.18-3.567.70.0719.73289842620.071100
3.56-4.117.70.0513.12909937830.05100
4.11-5.037.60.0415.32454632170.04100
5.03-7.127.40.03516.21890225390.035100
7.12-29.7356.70.03314.3962214430.03397.7

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 3.3 Å / D res low: 19.93 Å / FOM : 0.242 / FOM acentric: 0.281 / FOM centric: 0 / Reflection: 13637 / Reflection acentric: 11732 / Reflection centric: 1905
Phasing MAD setR cullis acentric: 1.73 / R cullis centric: 1 / Highest resolution: 3.3 Å / Lowest resolution: 19.93 Å / Loc acentric: 0 / Loc centric: 0 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 11732 / Reflection centric: 1905
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
12.23-19.931.030.10.114887
8.82-12.231.120.10.1354136
6.9-8.821.460.10.1646168
5.66-6.91.810.101025224
4.8-5.661.40.101498261
4.17-4.81.48002038304
3.68-4.172.33002634339
3.3-3.687.9003389386
Phasing MAD set site

Atom type symbol: SE / B iso: 65.988 / Occupancy iso: 0

IDFract xFract yFract zOccupancy
1-0.566-0.348-0.1663.787
2-0.713-0.522-0.3573.479
3-0.423-0.207-0.2051.932
4-0.909-0.53-0.4941.364
5-0.474-0.392-0.1620.936
6-0.446-0.549-0.3880.756
7-0.777-0.554-0.3030.69
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.23-19.930.3130.497023514887
8.82-12.230.3540.490490354136
6.9-8.820.3950.4980814646168
5.66-6.90.3860.47012491025224
4.8-5.660.3570.419017591498261
4.17-4.80.2950.339023422038304
3.68-4.170.1940.219029732634339
3.3-3.680.0940.105037753389386
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 21966
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.89-10070.60.714501
7.95-9.8966.60.709503
6.95-7.95630.685506
6.31-6.9563.50.714506
5.82-6.3161.70.745548
5.44-5.8264.60.731584
5.12-5.4457.50.783616
4.85-5.1258.50.806656
4.62-4.85610.766667
4.42-4.62610.755719
4.24-4.4260.60.736749
4.09-4.2465.30.727757
3.95-4.0962.30.675775
3.82-3.9568.50.669822
3.7-3.8266.80.603795
3.6-3.771.60.698851
3.5-3.677.10.576874
3.41-3.5780.541904
3.33-3.4174.50.449941
3.25-3.3384.10.388949
3.18-3.2590.70.533999
3.11-3.1889.80.465975
3.05-3.11890.4051033
2.99-3.0590.10.321035
2.93-2.9987.90.4621074
2.88-2.9386.50.1121060
2.8-2.8888.80.3751567

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
MLPHAREphasing
DMphasing
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.15data extraction
StructureStudiodata collection
RefinementMethod to determine structure: SAD / Resolution: 2.25→27.796 Å / SU ML: 0.23 / σ(F): 0.83 / Phase error: 20.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 8093 10.09 %RANDOM
Rwork0.187 ---
all0.1893 42289 --
obs0.1893 42227 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.88 Å2 / Biso mean: 27.27 Å2 / Biso min: 11.44 Å2
Refinement stepCycle: LAST / Resolution: 2.25→27.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5621 0 0 348 5969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055751
X-RAY DIFFRACTIONf_angle_d1.0637756
X-RAY DIFFRACTIONf_chiral_restr0.048832
X-RAY DIFFRACTIONf_plane_restr0.003997
X-RAY DIFFRACTIONf_dihedral_angle_d15.6892112
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.27560.29622670.243924552722100
2.2756-2.30230.28173370.228923582695100
2.3023-2.33040.28152190.219124182637100
2.3304-2.35990.23143120.214823842696100
2.3599-2.39090.282590.221324122671100
2.3909-2.42370.24872560.20824272683100
2.4237-2.45830.23682690.220424022671100
2.4583-2.49490.28122500.214824162666100
2.4949-2.53390.252940.21323922686100
2.5339-2.57540.26082620.212224242686100
2.5754-2.61980.24313090.219623412650100
2.6198-2.66740.22773110.208723622673100
2.6674-2.71860.2542830.198623702653100
2.7186-2.77410.24732370.20524552692100
2.7741-2.83440.2413130.216423442657100
2.8344-2.90020.24162280.198524662694100
2.9002-2.97270.24382530.198624122665100
2.9727-3.05290.23722650.217723982663100
3.0529-3.14270.26682160.225424992715100
3.1427-3.2440.22042260.205624092635100
3.244-3.35970.2382870.205423842671100
3.3597-3.4940.20672510.199624212672100
3.494-3.65270.18952780.167723872665100
3.6527-3.84480.17793040.157923982702100
3.8448-4.0850.1842400.162324072647100
4.085-4.39920.17822850.151724142699100
4.3992-4.83980.1562740.138423962670100
4.8398-5.53540.14642740.157523772651100
5.5354-6.95590.18772450.17624532698100
6.9559-27.79790.15352890.15362355264499

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