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- PDB-5j3n: C-terminal domain of EcoR124I HsdR subunit fused with the pH-sens... -

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Basic information

Entry
Database: PDB / ID: 5j3n
TitleC-terminal domain of EcoR124I HsdR subunit fused with the pH-sensitive GFP variant ratiometric pHluorin
ComponentsGreen fluorescent protein,HsdR
KeywordsHYDROLASE / HsdR / EcoR124I / type I restriction-modification system / pHluorin / GFP / fusion protein
Function / homology
Function and homology information


type I site-specific deoxyribonuclease / type I site-specific deoxyribonuclease activity / DNA restriction-modification system / bioluminescence / generation of precursor metabolites and energy / DNA binding / ATP binding
Similarity search - Function
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 / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP ...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 / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein / Type I restriction enzyme EcoR124I/EcoR124II endonuclease subunit
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsGrinkevich, P. / Iermak, I. / Luedtke, N. / Mesters, J.R. / Ettrich, R. / Ludwig, J.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Czech Science FoundationP207/12/2323 Czech Republic
MEYSLM2015055 Czech Republic
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding.
Authors: Grinkevich, P. / Sinha, D. / Iermak, I. / Guzanova, A. / Weiserova, M. / Ludwig, J. / Mesters, J.R. / Ettrich, R.H.
History
DepositionMar 31, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Aug 22, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein,HsdR
B: Green fluorescent protein,HsdR


Theoretical massNumber of molelcules
Total (without water)90,9832
Polymers90,9832
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-9 kcal/mol
Surface area26500 Å2
2
A: Green fluorescent protein,HsdR
B: Green fluorescent protein,HsdR

A: Green fluorescent protein,HsdR
B: Green fluorescent protein,HsdR


Theoretical massNumber of molelcules
Total (without water)181,9654
Polymers181,9654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area10050 Å2
ΔGint-32 kcal/mol
Surface area48260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.386, 176.505, 126.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Green fluorescent protein,HsdR


Mass: 45491.281 Da / Num. of mol.: 2 / Fragment: UNP Residues 2-238, 887-1038
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Escherichia coli (E. coli)
Gene: GFP, hsdR / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: P42212, UniProt: Q304R3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% (w/v) PEG 3350, 0.2 M KH2PO4, 4% v/v acetone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 34464 / % possible obs: 99.2 % / Redundancy: 4.68 % / Biso Wilson estimate: 41.27 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Net I/σ(I): 11.7
Reflection shellResolution: 2.45→2.59 Å / Redundancy: 4.63 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.74 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSOct 15, 2015data reduction
MOLREP11.4.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W7S

1w7s


Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.955 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.248 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25383 1716 5 %RANDOM
Rwork0.19194 ---
obs0.1949 32725 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.959 Å2
Baniso -1Baniso -2Baniso -3
1-6.33 Å20 Å2-0 Å2
2---2.99 Å20 Å2
3----3.34 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4810 0 0 198 5008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194935
X-RAY DIFFRACTIONr_bond_other_d0.0020.024493
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.9476680
X-RAY DIFFRACTIONr_angle_other_deg1.003310330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7915613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37424.895239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47415791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.091518
X-RAY DIFFRACTIONr_chiral_restr0.0950.2727
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025663
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021153
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0564.0852461
X-RAY DIFFRACTIONr_mcbond_other3.0544.0842460
X-RAY DIFFRACTIONr_mcangle_it4.7716.1223061
X-RAY DIFFRACTIONr_mcangle_other4.776.1233062
X-RAY DIFFRACTIONr_scbond_it3.294.1412474
X-RAY DIFFRACTIONr_scbond_other3.2894.1422475
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1756.1133618
X-RAY DIFFRACTIONr_long_range_B_refined7.10830.9325345
X-RAY DIFFRACTIONr_long_range_B_other7.11330.9365292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.446→2.509 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 134 -
Rwork0.347 2206 -
obs--94.09 %

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