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- PDB-1ckq: PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAATTCG... -

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Basic information

Entry
Database: PDB / ID: 1ckq
TitlePRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAATTCGCG) COMPLEX
Components
  • DNA (5'-D(*TP*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
  • PROTEIN (ENDONUCLEASE)
KeywordsPROTEIN/DNA / SEQUENCE-SPECIFIC DNA-PROTEIN COMPLEX / PROTEIN-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 / DNA (> 10) / Type II restriction enzyme EcoRI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.85 Å
AuthorsHorvath, M. / 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. / Choi, J. / Kim, Y. / Wilkosz, P.A. / Chandrasekhar, K. / Rosenberg, J.M.
History
DepositionApr 22, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 26, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: DNA (5'-D(*TP*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
A: PROTEIN (ENDONUCLEASE)


Theoretical massNumber of molelcules
Total (without water)34,9382
Polymers34,9382
Non-polymers00
Water2,720151
1
B: DNA (5'-D(*TP*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
A: PROTEIN (ENDONUCLEASE)

B: DNA (5'-D(*TP*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
A: PROTEIN (ENDONUCLEASE)


Theoretical massNumber of molelcules
Total (without water)69,8764
Polymers69,8764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)118.110, 118.110, 49.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Cell settingtrigonal
Space group name H-MP321
DetailsECO RI IS A DIMER. THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONSISTS OF A MONOMER AND THE COORDINATES OF THIS MONOMER ARE PRESENTED IN THIS ENTRY. TO GENERATE THE DIMER AND THE OTHER HALF OF THE DNA DUPLEX ONE MUST APPLY THE FOLLOWING CRYSTALLOGRAPHIC TWO-FOLD TRANSFORMATION TO THE COORDINATES IN THIS ENTRY - -.5 .866025 0.0 .866025 .5 0.0 0.0 0.0 -1.0

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Components

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


Mass: 3967.585 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein PROTEIN (ENDONUCLEASE)


Mass: 30970.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P00642
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST 15 RESIDUES ARE DISORDERED IN THE CRYSTAL STRUCTURE AND NOT SEEN IN THE ELECTRON DENSITY.

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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: 2.84 Å3/Da / Density % sol: 58 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5 / Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.1
DetectorDetector: IMAGE PLATE / Date: Apr 15, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.85→8 Å / Num. obs: 32270 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 22.2
Reflection shellResolution: 1.85→1.91 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2 / % possible all: 91.1

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1ERI

1eri


Resolution: 1.85→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: RFREE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.286 3025 10 %RANDOM
Rwork0.235 ---
obs0.235 27076 99 %-
Displacement parametersBiso mean: 38.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-8 Å
Luzzati sigma a0.31 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 263 0 151 2465
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.003
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_deg1.026
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_d0.889
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
LS refinement shellResolution: 1.85→1.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3858 109 12 %
Rwork0.3798 801 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH19.PEP
X-RAY DIFFRACTION3DNA-RNA.PARAMTOPH11.WAT
X-RAY DIFFRACTION4DNA-RNA.TOP

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