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- PDB-4xjx: STRUCTURE OF MUTANT (E165H) OF THE HSDR SUBUNIT OF THE ECOR124I R... -

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Entry
Database: PDB / ID: 4xjx
TitleSTRUCTURE OF MUTANT (E165H) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP
ComponentsHsdR
KeywordsHYDROLASE / Restriction enzyme / ATP
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 / Restriction endonuclease, type I, HsdR ...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 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 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 / molecular replacement / Resolution: 2.4 Å
AuthorsBaikova, T. / Stsiapanava, A. / Moche, M. / Degtjarik, O. / Kuta-Smatanova, I. / Ettrich, R.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science FoundationP207/12/2323 Czech Republic
CitationJournal: To Be Published
Title: STRUCTURE OF MUTANT (E165H) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP
Authors: Baikova, T. / Ettrich, R.
History
DepositionJan 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
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_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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HsdR
B: HsdR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,6396
Polymers240,5762
Non-polymers1,0634
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-13 kcal/mol
Surface area73410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.221, 124.542, 128.540
Angle α, β, γ (deg.)90.000, 107.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HsdR


Mass: 120287.906 Da / Num. of mol.: 2 / Fragment: UNP residues 1-1038 / Mutation: E165H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hsdR / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q304R3, UniProt: P10486*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 3.17 Å3/Da / Density % sol: 61.15 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 5 ul protein solution were mixed with 2 ul reservoir solution containing 13% (w/v) PEG 4000, 22% glycerol, 0.08 M MES, 2mM DDT, and 0.7 ul of 0.1 M sodium bromide as additive
PH range: 5.7-5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.4→49.09 Å / Num. obs: 99544 / % possible obs: 99.2 % / Redundancy: 4.14 % / Biso Wilson estimate: 46.39 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 9.37
Reflection shellResolution: 2.4→2.54 Å / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.65 / % possible all: 96.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.15 Å49.09 Å
Translation8.15 Å49.09 Å

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHASER2.5.5phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W00

2w00


Resolution: 2.4→49.09 Å / Cor.coef. Fo:Fc: 0.8858 / Cor.coef. Fo:Fc free: 0.8677 / SU R Cruickshank DPI: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.287 / SU Rfree Blow DPI: 0.218 / SU Rfree Cruickshank DPI: 0.224
RfactorNum. reflection% reflectionSelection details
Rfree0.2435 4975 5 %RANDOM
Rwork0.2081 ---
obs0.2099 99487 99.66 %-
Displacement parametersBiso max: 151.13 Å2 / Biso mean: 54.82 Å2 / Biso min: 16.49 Å2
Baniso -1Baniso -2Baniso -3
1--21.7462 Å20 Å214.2055 Å2
2--15.1189 Å20 Å2
3---6.6273 Å2
Refine analyzeLuzzati coordinate error obs: 0.338 Å
Refinement stepCycle: final / Resolution: 2.4→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14127 0 64 471 14662
Biso mean--34.64 47.08 -
Num. residues----1724
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3033 359 5.01 %
Rwork0.2619 6807 -
all0.264 7166 -
obs--99.66 %

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