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- PDB-3evy: Crystal structure of a fragment of a putative type I restriction ... -

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Basic information

Entry
Database: PDB / ID: 3evy
TitleCrystal structure of a fragment of a putative type I restriction enzyme R protein from Bacteroides fragilis
ComponentsPutative type I restriction enzyme R protein
KeywordsHYDROLASE / STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
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
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #910 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #910 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Type I restriction enzyme R Protein
Similarity search - Component
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsBonanno, J.B. / Gilmore, M. / Bain, K.T. / Miller, S. / Sampathkumar, P. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a fragment of a putative type I restriction enzyme R protein from Bacteroides fragilis
Authors: Bonanno, J.B. / Gilmore, M. / Bain, K.T. / Miller, S. / Sampathkumar, P. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionOct 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: 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: Putative type I restriction enzyme R protein
B: Putative type I restriction enzyme R protein


Theoretical massNumber of molelcules
Total (without water)55,6972
Polymers55,6972
Non-polymers00
Water1,964109
1
A: Putative type I restriction enzyme R protein


Theoretical massNumber of molelcules
Total (without water)27,8481
Polymers27,8481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative type I restriction enzyme R protein


Theoretical massNumber of molelcules
Total (without water)27,8481
Polymers27,8481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.834, 56.470, 75.857
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsprobable monomer

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Components

#1: Protein Putative type I restriction enzyme R protein


Mass: 27848.344 Da / Num. of mol.: 2 / Fragment: residues 656-884
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Strain: ATCC 25285 / Gene: BF1836, hsdR / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LEB7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATE THAT IT IS POSSIBLE THAT WHAT CRYSTALLIZED WAS A PROTEOLYTIC FRAGMENT. THE MS DID NOT ...AUTHOR STATE THAT IT IS POSSIBLE THAT WHAT CRYSTALLIZED WAS A PROTEOLYTIC FRAGMENT. THE MS DID NOT INDICATE A FRAGMENT OF THE APPROXIMATE SIZE OF THE OBSERVED PORTION SO IT IS POSSIBLE FRAGMENTATION OCCURRED DURING THE CRYSTALLIZATION EXPERIMENT. THEREFORE, THE WHOLE SEQUENCE IS LEFT IN THE RECORD.

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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

Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 20% PEG 3350, 200mM potassium sulfate, pH 7.0, Vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 10, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.95→45.314 Å / Num. all: 17791 / Num. obs: 17791 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 9.5
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.6 / Num. measured all: 21701 / Num. unique all: 2554 / Rsym value: 0.59 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.301 / WRfactor Rwork: 0.273 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.741 / SU B: 4.984 / SU ML: 0.14 / SU R Cruickshank DPI: 0.17 / SU Rfree: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.17 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 900 5.1 %RANDOM
Rwork0.229 ---
obs0.231 17721 99.96 %-
all-17728 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 74.71 Å2 / Biso mean: 45.148 Å2 / Biso min: 30.13 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å20 Å20 Å2
2---0.85 Å20 Å2
3----2.06 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 0 109 1511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221428
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.9741915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.045165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.7523.65982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40415266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.851514
X-RAY DIFFRACTIONr_chiral_restr0.1320.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021100
X-RAY DIFFRACTIONr_mcbond_it1.2451.5833
X-RAY DIFFRACTIONr_mcangle_it2.26821335
X-RAY DIFFRACTIONr_scbond_it3.83595
X-RAY DIFFRACTIONr_scangle_it5.8594.5580
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 73 -
Rwork0.342 1192 -
all-1265 -
obs-1192 99.92 %

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