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- PDB-1qc9: THE CRYSTALLOGRAPHIC STRUCTURE OF RESTRICTION ENDONUCLEASE ECO RI... -

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Basic information

Entry
Database: PDB / ID: 1qc9
TitleTHE CRYSTALLOGRAPHIC STRUCTURE OF RESTRICTION ENDONUCLEASE ECO RI AT 3.3 A IN THE ABSENSE OF DNA
ComponentsPROTEIN (ECO RI ENDONUCLEASE)
KeywordsENDONUCLEASE / PROTEIN / RESTRICTION ENDONUCLEASE / APOENZYME
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
Type II restriction enzyme EcoRI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsChandrasekhar, K. / Horvath, M.M. / Samudzi, C. / Choi, J. / Rosenberg, J.M.
CitationJournal: To be Published
Title: The 3.3 A Crystallographic Structure of Restriction Endonuclease Eco RI in the Absence of DNA
Authors: Chandrasekhar, K. / Horvath, M.M. / Samudzi, C. / Choi, J. / Rosenberg, J.M.
History
DepositionMay 18, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Jun 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 1, 2017Group: Database references / Structure summary
Revision 1.4Feb 8, 2017Group: Derived calculations
Revision 1.5Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: PROTEIN (ECO RI ENDONUCLEASE)
B: PROTEIN (ECO RI ENDONUCLEASE)
C: PROTEIN (ECO RI ENDONUCLEASE)


Theoretical massNumber of molelcules
Total (without water)92,9113
Polymers92,9113
Non-polymers00
Water00
1
A: PROTEIN (ECO RI ENDONUCLEASE)

A: PROTEIN (ECO RI ENDONUCLEASE)


Theoretical massNumber of molelcules
Total (without water)61,9402
Polymers61,9402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4530 Å2
ΔGint-31 kcal/mol
Surface area23650 Å2
MethodPISA
2
B: PROTEIN (ECO RI ENDONUCLEASE)

C: PROTEIN (ECO RI ENDONUCLEASE)


Theoretical massNumber of molelcules
Total (without water)61,9402
Polymers61,9402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4480 Å2
ΔGint-31 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.680, 127.350, 49.870
Angle α, β, γ (deg.)90.00, 98.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (ECO RI ENDONUCLEASE)


Mass: 30970.184 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P00642, type II site-specific deoxyribonuclease

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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: 3.53 Å3/Da / Density % sol: 65.11 %

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.06→100 Å / Num. all: 24225 / Num. obs: 17576 / % possible obs: 72.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Biso Wilson estimate: 25.89 Å2 / Net I/σ(I): 20.41

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Processing

Software
NameVersionClassification
MERLOTphasing
X-PLOR3.1refinement
X-GENdata reduction
X-GENdata scaling
RefinementResolution: 3→8 Å / σ(F): 3 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.295 1609
Rwork0.251 -
all-26179
obs-14570
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5979 0 0 0 5979
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.573

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