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- PDB-1qps: THE CRYSTAL STRUCTURE OF A POST-REACTIVE COGNATE DNA-ECO RI COMPL... -

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Basic information

Entry
Database: PDB / ID: 1qps
TitleTHE CRYSTAL STRUCTURE OF A POST-REACTIVE COGNATE DNA-ECO RI COMPLEX AT 2.50 A IN THE PRESENCE OF MN2+ ION
Components
  • 5'-D(*AP*AP*TP*TP*CP*GP*CP*GP*)-3'
  • 5'-D(*TP*CP*GP*CP*GP*)-3'
  • ENDONUCLEASE ECORI
KeywordsHYDROLASE/DNA / ENZYME / RESTRICTION ENDONCULEASE / PROTEIN / 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 / magnesium ion binding / DNA binding
Similarity search - Function
Restriction endonuclease, type II, EcoRI / Restriction endonuclease, type II, EcoRI, Proteobacteria / Restriction endonuclease EcoRI / ECO RI Endonuclease; Chain A / Eco RI Endonuclease, subunit A / Restriction endonuclease, type II, EcoRI/MunI / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA / Type II restriction enzyme EcoRI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsHorvath, M. / Choi, J. / Kim, Y. / Wilkosz, P. / Rosenberg, J.M.
CitationJournal: To be Published
Title: The Integration of Recognition and Cleavage: X-Ray Structures of Pre- Transition State and Post-Reactive DNA-Eco RI Endonuclease Complexes
Authors: Horvath, M.M. / Choi, J. / Kim, Y. / Wilkosz, P. / Rosenberg, J.M.
History
DepositionMay 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 11, 2017Group: Other
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.6Feb 14, 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_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.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_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

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Assembly

Deposited unit
M: 5'-D(*TP*CP*GP*CP*GP*)-3'
N: 5'-D(*AP*AP*TP*TP*CP*GP*CP*GP*)-3'
A: ENDONUCLEASE ECORI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1504
Polymers33,0953
Non-polymers551
Water79344
1
M: 5'-D(*TP*CP*GP*CP*GP*)-3'
N: 5'-D(*AP*AP*TP*TP*CP*GP*CP*GP*)-3'
A: ENDONUCLEASE ECORI
hetero molecules

M: 5'-D(*TP*CP*GP*CP*GP*)-3'
N: 5'-D(*AP*AP*TP*TP*CP*GP*CP*GP*)-3'
A: ENDONUCLEASE ECORI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2998
Polymers66,1906
Non-polymers1102
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)118.4, 118.4, 49.7
Angle α, β, γ (deg.)90, 90, 120
Int Tables number150
Cell settingtrigonal
Space group name H-MP321

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Components

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


Mass: 1496.011 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RECOGNITION SEQUENCE
#2: DNA chain 5'-D(*AP*AP*TP*TP*CP*GP*CP*GP*)-3'


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RECOGNITION SEQUENCE
#3: Protein ENDONUCLEASE ECORI / TYPE II RESTRICTION ENZYME ECORI / R.ECORI


Mass: 29172.166 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-277 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P00642
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.02 Å3/Da / Density % sol: 59.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: MN ION WAS SOAKED INTO PRE-REACTIVE PROTEIN-DNA COCRYSTALS AND DNA CLEAVAGE OCCURED IN-CRYSTALLO, pH 7.5, VAPOR DIFFUSION, temperature 4K
Components of the solutionsName: MN

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 14659 / Num. obs: 8653 / % possible obs: 59 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 2
Reflection shellResolution: 2.5→2.7 Å / Rmerge(I) obs: 0.083 / % possible all: 13

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementResolution: 2.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 3
Stereochemistry target values: ENGH AND HUBER PARAMETERS FOR PROTEIN; BERMAN PARAMETERS FOR DNA
RfactorNum. reflection
all0.177 -
obs-7596
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 264 1 44 2360
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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