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- PDB-1cl8: A PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAPTT... -

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Basic information

Entry
Database: PDB / ID: 1cl8
TitleA PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAPTTCGCG) COMPLEX WITH DNA BASE ANALOG PURINE (P)
Components
  • DNA (5'-D(*TP*CP*GP*CP*GP*AP*(PRN)P*TP*TP*CP*GP*CP*G)-3')
  • PROTEIN (ENDONUCLEASE)
KeywordsPROTEIN/DNA / ENDONUCLEASE/DNA / DNA BASE ANALOG / 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: 1.8 Å
AuthorsHorvath, M. / Rosenberg, J.M.
CitationJournal: To be Published
Title: Iap (Inner-Adenine to Purine): A Cognate EcoRI-DNA Base Analog Complex
Authors: Horvath, M. / Rosenberg, J.M.
History
DepositionMay 6, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 19, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,9232
Polymers34,9232
Non-polymers00
Water2,792155
1
B: DNA (5'-D(*TP*CP*GP*CP*GP*AP*(PRN)P*TP*TP*CP*GP*CP*G)-3')
A: PROTEIN (ENDONUCLEASE)

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


Theoretical massNumber of molelcules
Total (without water)69,8464
Polymers69,8464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)117.833, 117.833, 48.989
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Cell settingtrigonal
Space group name H-MP321

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Components

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


Mass: 3952.570 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 / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPRN IS ADENINE WITH THE N6 AMINO GROUP REMOVED

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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: 2.8 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: 1.8→8 Å / Num. obs: 35192 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 19.3
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.6 / % possible all: 91

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Processing

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

1ckq


Resolution: 1.8→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: RFREE / σ(F): 2
Details: DNA-RNA.PARAM WAS MODIFIED TO CONTAIN A MODIFIED RESIDUE PRN
RfactorNum. reflection% reflectionSelection details
Rfree0.287 3528 10 %RANDOM
Rwork0.243 ---
obs0.243 35192 98.3 %-
Displacement parametersBiso mean: 36.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.34 Å
Luzzati d res low-8 Å
Luzzati sigma a0.3 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 262 0 158 2471
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
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_deg1.067
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_d0.805
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: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3576 326 10.1 %
Rwork0.3568 2898 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH19.PEP
X-RAY DIFFRACTION3MODIFIED DNA-RNA.PARAMTOPH11.WAT
X-RAY DIFFRACTION4DNA-RNA.TOP

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