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- PDB-4abt: Crystal structure of Type IIF restriction endonuclease NgoMIV wit... -

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Basic information

Entry
Database: PDB / ID: 4abt
TitleCrystal structure of Type IIF restriction endonuclease NgoMIV with cognate uncleaved DNA
Components
  • 5'-D(*TP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP)-3'
  • TYPE-2 RESTRICTION ENZYME NGOMIV
KeywordsHYDROLASE/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
DNA / DNA (> 10) / Type II restriction enzyme NgoMIV
Similarity search - Component
Biological speciesNEISSERIA GONORRHOEAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsManakova, E.N. / Grazulis, S. / Zaremba, M. / Tamulaitiene, G. / Golovenko, D. / Siksnys, V.
Citation
Journal: To be Published
Title: Structure of Type Iif Restriction Endonuclease Ngomiv with Cognate Uncleaved DNA
Authors: Manakova, E.N. / Grazulis, S. / Zaremba, M. / Tamulaitiene, G. / Golovenko, D. / Siksnys, V.
#1: Journal: Nucleic Acids Res. / Year: 2012
Title: Structural Mechanisms of the Degenerate Sequence Recognition by Bse634I Restriction Endonuclease.
Authors: Manakova, E. / Grazulis, S. / Zaremba, M. / Tamulaitiene, G. / Golovenko, D. / Siksnys, V.
History
DepositionDec 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references / Other
Revision 1.2Jul 17, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_special_symmetry ...diffrn_source / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_symmetry / _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: TYPE-2 RESTRICTION ENZYME NGOMIV
B: TYPE-2 RESTRICTION ENZYME NGOMIV
E: 5'-D(*TP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP)-3'
G: 5'-D(*TP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4447
Polymers70,3244
Non-polymers1203
Water4,432246
1
A: TYPE-2 RESTRICTION ENZYME NGOMIV
B: TYPE-2 RESTRICTION ENZYME NGOMIV
E: 5'-D(*TP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP)-3'
G: 5'-D(*TP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP)-3'
hetero molecules

A: TYPE-2 RESTRICTION ENZYME NGOMIV
B: TYPE-2 RESTRICTION ENZYME NGOMIV
E: 5'-D(*TP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP)-3'
G: 5'-D(*TP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,88914
Polymers140,6488
Non-polymers2406
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area29170 Å2
ΔGint-155 kcal/mol
Surface area40210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.899, 90.081, 92.711
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11E-1000-

CA

21A-2077-

HOH

31A-2094-

HOH

41B-2076-

HOH

51G-2007-

HOH

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Components

#1: Protein TYPE-2 RESTRICTION ENZYME NGOMIV / TYPE IIF RESTRICTION ENDONUCLEASE NGOMIV / R.NGOMIV / ENDONUCLEASE NGOMIV / TYPE II RESTRICTION ENZYME NGOMIV


Mass: 31810.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA GONORRHOEAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS 174 DE3
References: UniProt: P31032, type II site-specific deoxyribonuclease
#2: DNA chain 5'-D(*TP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP)-3'


Mass: 3351.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) NEISSERIA GONORRHOEAE (bacteria)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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 Å3/Da / Density % sol: 39.1 % / Description: NONE
Crystal growpH: 7.5 / Details: NAHEPES 0.1M, CACL2 0.2M, MPD 24%, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.812
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 3, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 2.22→11.95 Å / Num. obs: 28869 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8
Reflection shellResolution: 2.22→2.27 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.8 / % possible all: 84.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FIU

1fiu


Resolution: 2.22→11.95 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23483 2859 9.9 %RANDOM
Rwork0.18003 ---
obs0.18543 25981 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.898 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2---0.62 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.22→11.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 444 3 246 5169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224836
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8152.0766655
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4775549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02324.216204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77315726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8841534
X-RAY DIFFRACTIONr_chiral_restr0.1080.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213516
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9461.52752
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.74424420
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.71732084
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1614.52233
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.215→2.271 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 206 -
Rwork0.272 1562 -
obs--85.58 %

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