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- PDB-6h2j: Crystal structure of the HsdR subunit of the EcoR124I restriction... -

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Basic information

Entry
Database: PDB / ID: 6h2j
TitleCrystal structure of the HsdR subunit of the EcoR124I restriction enzyme with the C-terminal domain
ComponentsType I restriction enzyme R Protein
KeywordsHYDROLASE / EcoR124 / HsdR / C-terminal domain / restriction-modification enzyme / endonuclease / Escherichia coli
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 / Resolution: 2.6 Å
AuthorsGrinkevich, P. / Mesters, J.R. / Ettrich, R.H.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science FoundationP207/12/2323 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
DepositionJul 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 17, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type I restriction enzyme R Protein
B: Type I restriction enzyme R Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,0286
Polymers241,9652
Non-polymers1,0634
Water6,900383
1
A: Type I restriction enzyme R Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,5143
Polymers120,9821
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type I restriction enzyme R Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,5143
Polymers120,9821
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.910, 129.922, 161.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Type I restriction enzyme R Protein


Mass: 120982.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hsdR / Production host: Escherichia coli (E. coli)
References: UniProt: Q304R3, UniProt: P10486*PLUS, type I site-specific deoxyribonuclease
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.987 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 80316 / % possible obs: 100 % / Redundancy: 9.4 % / Net I/σ(I): 18.2
Reflection shellResolution: 2.6→2.64 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2w00, 5j3n

2w00

5j3n


Resolution: 2.6→19.968 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 977 1.22 %
Rwork0.2027 --
obs0.2035 80202 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→19.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14917 0 64 383 15364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915263
X-RAY DIFFRACTIONf_angle_d1.00820599
X-RAY DIFFRACTIONf_dihedral_angle_d5.4139216
X-RAY DIFFRACTIONf_chiral_restr0.0532262
X-RAY DIFFRACTIONf_plane_restr0.0062664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.73680.34911230.258611173X-RAY DIFFRACTION100
2.7368-2.90770.28741440.239511192X-RAY DIFFRACTION100
2.9077-3.13150.29341230.23111248X-RAY DIFFRACTION100
3.1315-3.44510.28721330.213911294X-RAY DIFFRACTION100
3.4451-3.94030.25961530.189711281X-RAY DIFFRACTION100
3.9403-4.95190.23511350.171611373X-RAY DIFFRACTION100
4.9519-19.96860.2421660.198711664X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.52520.70550.3580.9231-0.19260.9216-0.0268-0.11530.28460.0779-0.00470.0227-0.0177-0.03530.00110.30530.00590.01280.2832-0.01860.337733.77545.824630.086
21.1776-0.16540.06613.23311.04322.2384-0.03720.3031-0.2066-0.42360.0475-0.18030.08580.178-00.37780.00250.00860.4022-0.0090.292255.977628.551114.9611
32.75320.31820.59872.75020.1121.35060.2195-0.1174-0.50350.1448-0.0965-0.38910.36870.12030.0020.4549-0.0088-0.07840.32430.03990.442268.716119.69140.9436
42.3839-0.7611-0.59732.58841.12032.4956-0.0481-0.4716-0.04790.6876-0.0762-0.0121-0.1851-0.15730.00050.512-0.0848-0.07550.50650.02590.425466.298943.679855.5524
53.1728-0.78260.3340.24810.08070.97310.0023-0.0195-0.281-0.00420.0031-0.02790.13560.02230.0010.37010.0009-0.01730.3441-0.04050.289334.5835-12.695326.4665
63.14120.531-0.19511.71740.24660.2652-0.0728-0.3469-0.41960.28050.01210.04070.0977-0.07940.00380.35840.0384-0.03970.41450.01590.312224.84-14.998334.7004
71.6037-0.42460.24843.0788-0.41130.8634-0.13350.30010.1635-0.22980.12720.1343-0.1376-0.02480.00060.3251-0.0796-0.05810.4488-0.01620.26139.8380.979316.3236
81.35480.2519-1.15741.41980.33241.11570.0060.35730.1302-0.29430.05360.4217-0.0128-0.34220.00460.3304-0.0071-0.10180.39670.01880.4027-4.5191-4.292922.1447
93.1820.1942-0.51723.0382-0.37780.34270.1101-0.1830.57040.18020.04350.6611-0.4891-0.33810.00030.51980.040.11840.4044-0.03110.706-11.395513.357543.3995
101.31370.6025-0.49551.4291-0.98652.12630.12670.0060.19240.17110.00250.3472-0.12420.06270.00080.3252-0.00090.04240.3081-0.04330.3786-3.82010.89341.314
110.99460.57341.13671.833-0.55272.6135-0.104-0.55490.27610.7342-0.12660.24930.0015-0.22920.00090.6328-0.10480.09560.5963-0.02760.4465-3.6141-9.849661.4781
121.79240.50691.21250.15120.2061.5438-0.1355-0.44230.15540.52680.0625-0.56240.04760.5783-0.00091.0081-0.0862-0.1641.1017-0.03820.799725.8921-6.663467.1512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 259 )
2X-RAY DIFFRACTION2chain 'A' and (resid 260 through 468 )
3X-RAY DIFFRACTION3chain 'A' and (resid 469 through 699 )
4X-RAY DIFFRACTION4chain 'A' and (resid 700 through 885 )
5X-RAY DIFFRACTION5chain 'B' and (resid 13 through 122 )
6X-RAY DIFFRACTION6chain 'B' and (resid 123 through 225 )
7X-RAY DIFFRACTION7chain 'B' and (resid 226 through 425 )
8X-RAY DIFFRACTION8chain 'B' and (resid 426 through 483 )
9X-RAY DIFFRACTION9chain 'B' and (resid 484 through 605 )
10X-RAY DIFFRACTION10chain 'B' and (resid 606 through 771 )
11X-RAY DIFFRACTION11chain 'B' and (resid 772 through 859 )
12X-RAY DIFFRACTION12chain 'B' and (resid 860 through 1030 )

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