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- PDB-1fiu: TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA -

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Basic information

Entry
Database: PDB / ID: 1fiu
TitleTETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA
Components
  • DNA (5'-D(*TP*GP*CP*G)-3')
  • DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3')
  • TYPE II RESTRICTION ENZYME NGOMI
Keywordshydrolase/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / RESTRICTION ENDONUCLEASE / RESTRICTION-MODIFICTION SYSTEMS / HYDROLASE / PHOSPHODIESTERASE / METAL ION / COMPLEX (ENDONUCLEASE-DNA) / hydrolase-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / metal ion binding
Similarity search - Function
Type-2 restriction enzyme NgoMIV / Type-2 restriction enzyme NgoMIV / Type-2 restriction enzyme NgoMIV superfamily / NgoMIV restriction enzyme / Restriction endonuclease type II-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / DNA / Type II restriction enzyme NgoMIV
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsDeibert, M. / Grazulis, S. / Sasnauskas, G. / Siksnys, V. / Huber, R.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA.
Authors: Deibert, M. / Grazulis, S. / Sasnauskas, G. / Siksnys, V. / Huber, R.
History
DepositionAug 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
E: DNA (5'-D(*TP*GP*CP*G)-3')
I: DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3')
F: DNA (5'-D(*TP*GP*CP*G)-3')
J: DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3')
G: DNA (5'-D(*TP*GP*CP*G)-3')
K: DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3')
H: DNA (5'-D(*TP*GP*CP*G)-3')
L: DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3')
A: TYPE II RESTRICTION ENZYME NGOMI
B: TYPE II RESTRICTION ENZYME NGOMI
C: TYPE II RESTRICTION ENZYME NGOMI
D: TYPE II RESTRICTION ENZYME NGOMI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,90324
Polymers140,46812
Non-polymers43512
Water23,0411279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.400, 91.130, 149.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsThe biological assembly is a tetramer

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Components

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DNA chain , 2 types, 8 molecules EFGHIJKL

#1: DNA chain
DNA (5'-D(*TP*GP*CP*G)-3')


Mass: 1206.829 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: DNA chain
DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3')


Mass: 2099.387 Da / Num. of mol.: 4 / Source method: obtained synthetically

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Protein , 1 types, 4 molecules ABCD

#3: Protein
TYPE II RESTRICTION ENZYME NGOMI / E.C.3.1.21.4 / NGOMIV RESTRICTION ENDONUCLEASE / ENDONUCLEASE NGOMI / R.NGOMI


Mass: 31810.902 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Plasmid: PET15B / Production host: Escherichia coli (E. coli)
References: UniProt: P31032, type II site-specific deoxyribonuclease

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Non-polymers , 3 types, 1291 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1279 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MES 100mM, MgCl2 200mM, MPD 25%, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2MgCl211
3MPD11
4MES12
5MgCl212
6MPD12
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
125 %(v/w)MPD1reservoir
2200 mM1reservoirMgCl2
30.1 MMES1reservoirpH6.5
40.2 mMprotein1drop
520 mMTris-HCl1droppH7.5
6200 mM1dropNaCl
70.02 %(w/v)1dropNaN3

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.0697
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 21, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0697 Å / Relative weight: 1
ReflectionResolution: 1.6→17.26 Å / Num. all: 162845 / Num. obs: 160528 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 15.7 % / Rmerge(I) obs: 0.047
Reflection shellHighest resolution: 1.6 Å / % possible all: 88.7
Reflection
*PLUS
Num. measured all: 2553379
Reflection shell
*PLUS
% possible obs: 88.7 %

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Processing

Software
NameClassification
SHARPphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.6→17.26 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 16061 10 %RANDOM
Rwork0.1729 ---
all-162845 --
obs-160612 --
Refinement stepCycle: LAST / Resolution: 1.6→17.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8952 892 8 1295 11147
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.567
X-RAY DIFFRACTIONc_bond_d0.01
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg

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