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- PDB-4be7: MUTANT (K220R) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION EN... -

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Basic information

Entry
Database: PDB / ID: 4be7
TitleMUTANT (K220R) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP
ComponentsTYPE I RESTRICTION ENZYME ECOR124II R PROTEIN
KeywordsHYDROLASE / DNA RESTRICTION / DNA MODIFICATION
Function / homology
Function and homology information


type I site-specific deoxyribonuclease / type I site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / ATP binding
Similarity search - Function
tt1808, chain A - #50 / Actin; Chain A, domain 4 - #50 / tt1808, chain A / Restriction endonuclease, type I, HsdR, N-terminal / Type I restriction enzyme R protein, C-terminal / SWI2/SNF2 ATPase / : / Type I restriction enzyme R protein N terminus (HSDR_N) / Type I restriction and modification enzyme - subunit R C terminal / SWI2/SNF2 ATPase ...tt1808, chain A - #50 / Actin; Chain A, domain 4 - #50 / tt1808, chain A / Restriction endonuclease, type I, HsdR, N-terminal / Type I restriction enzyme R protein, C-terminal / SWI2/SNF2 ATPase / : / Type I restriction enzyme R protein N terminus (HSDR_N) / Type I restriction and modification enzyme - subunit R C terminal / SWI2/SNF2 ATPase / UvrB domain 3 / Restriction endonuclease, type I, HsdR / Actin; Chain A, domain 4 / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Complex / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Type I restriction enzyme EcoR124I/EcoR124II endonuclease subunit / Type I restriction enzyme EcoR124I/EcoR124II endonuclease subunit
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.744 Å
AuthorsCsefalvay, E. / Lapkouski, M. / Guzanova, A. / Csefalvay, L. / Baikova, T. / Shevelev, I. / Janscak, P. / Smatanova, I.K. / Panjikar, S. / Carey, J. ...Csefalvay, E. / Lapkouski, M. / Guzanova, A. / Csefalvay, L. / Baikova, T. / Shevelev, I. / Janscak, P. / Smatanova, I.K. / Panjikar, S. / Carey, J. / Weiserova, M. / Ettrich, R.
CitationJournal: Plos One / Year: 2015
Title: Functional Coupling of Duplex Translocation to DNA Cleavage in a Type I Restriction Enzyme.
Authors: Csefalvay, E. / Lapkouski, M. / Guzanova, A. / Csefalvay, L. / Baikova, T. / Shevelev, I. / Bialevich, V. / Shamayeva, K. / Janscak, P. / Kuta Smatanova, I. / Panjikar, S. / Carey, J. / ...Authors: Csefalvay, E. / Lapkouski, M. / Guzanova, A. / Csefalvay, L. / Baikova, T. / Shevelev, I. / Bialevich, V. / Shamayeva, K. / Janscak, P. / Kuta Smatanova, I. / Panjikar, S. / Carey, J. / Weiserova, M. / Ettrich, R.
History
DepositionMar 6, 2013Deposition site: PDBE / Processing site: PDBE
SupersessionMar 26, 2014ID: 2W74
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...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 / 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_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_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_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_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

Downloads & links

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Assembly

Deposited unit
B: TYPE I RESTRICTION ENZYME ECOR124II R PROTEIN
D: TYPE I RESTRICTION ENZYME ECOR124II R PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,05710
Polymers240,6142
Non-polymers1,4438
Water1,40578
1
B: TYPE I RESTRICTION ENZYME ECOR124II R PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,0285
Polymers120,3071
Non-polymers7214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: TYPE I RESTRICTION ENZYME ECOR124II R PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,0285
Polymers120,3071
Non-polymers7214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.045, 124.354, 128.012
Angle α, β, γ (deg.)90.00, 108.86, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.7512, 0.0107, -0.6599), (0.01269, -0.9999, -0.00176), (-0.6599, -0.007055, -0.7513)
Vector: 23.1334, -47.7764, 60.2134)

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Components

#1: Protein TYPE I RESTRICTION ENZYME ECOR124II R PROTEIN / R.ECOR124II / TYPE I RESTRICTION ENZYME ECOR124II R PROTEIN HSDR


Mass: 120306.875 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q304R3, UniProt: P10486*PLUS, type I site-specific deoxyribonuclease
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.72 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1 UL OF PROTEIN IN 20 MM PHOSPHATE PH 7.5, 100 MM KCL, 5 MM ATP WAS MIXED WITH 2 UL OF RESERVOIR, CONTAINING 0.2 M LI2SO4, 8 % PEG 20K, 8 % PEG 550 MME, 1.5 MM DTT, 277 K, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8126
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8126 Å / Relative weight: 1
ReflectionResolution: 2.72→68 Å / Num. obs: 63203 / % possible obs: 91.5 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 42.14 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.1
Reflection shellResolution: 2.72→2.87 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.9 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W00

2w00


Resolution: 2.744→32.358 Å / SU ML: 0.44 / σ(F): 1.38 / Phase error: 31.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2923 3190 5.1 %
Rwork0.2495 --
obs0.2517 62959 93.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 2.744→32.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13225 0 84 78 13387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413564
X-RAY DIFFRACTIONf_angle_d1.05518372
X-RAY DIFFRACTIONf_dihedral_angle_d15.6174877
X-RAY DIFFRACTIONf_chiral_restr0.0742047
X-RAY DIFFRACTIONf_plane_restr0.0032374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7438-2.78470.4465850.37421538X-RAY DIFFRACTION56
2.7847-2.82820.35781530.32232603X-RAY DIFFRACTION94
2.8282-2.87450.38971350.28682640X-RAY DIFFRACTION95
2.8745-2.92410.33071480.27642685X-RAY DIFFRACTION96
2.9241-2.97720.3251310.27482665X-RAY DIFFRACTION96
2.9772-3.03440.34661290.26822659X-RAY DIFFRACTION95
3.0344-3.09630.33051420.27142676X-RAY DIFFRACTION96
3.0963-3.16360.30751430.25892622X-RAY DIFFRACTION96
3.1636-3.23710.32021250.27012661X-RAY DIFFRACTION95
3.2371-3.3180.31821370.26712654X-RAY DIFFRACTION96
3.318-3.40760.3031610.25112624X-RAY DIFFRACTION95
3.4076-3.50780.321370.27072702X-RAY DIFFRACTION96
3.5078-3.62080.31081340.2432636X-RAY DIFFRACTION95
3.6208-3.75010.30191190.23392678X-RAY DIFFRACTION95
3.7501-3.90.28641660.22842645X-RAY DIFFRACTION95
3.9-4.07710.2571340.23562632X-RAY DIFFRACTION95
4.0771-4.29160.26381530.22262650X-RAY DIFFRACTION95
4.2916-4.55980.24811450.2142644X-RAY DIFFRACTION95
4.5598-4.91080.24731480.20822684X-RAY DIFFRACTION96
4.9108-5.40290.28071640.22012660X-RAY DIFFRACTION96
5.4029-6.180.27571370.25112676X-RAY DIFFRACTION95
6.18-7.76830.28821360.2482667X-RAY DIFFRACTION95
7.7683-32.36050.25871280.28982468X-RAY DIFFRACTION86

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