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- PDB-3aly: Crystal Structure of RNase HI from Sulfolobus tokodaii with C-ter... -

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Basic information

Entry
Database: PDB / ID: 3aly
TitleCrystal Structure of RNase HI from Sulfolobus tokodaii with C-terminal deletion
ComponentsPutative uncharacterized protein ST0753
KeywordsHYDROLASE / thermostable RNase HI / C-terminal anchor deletion
Function / homology
Function and homology information


ribonuclease H / RNA-DNA hybrid ribonuclease activity / DNA binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Reverse transcriptase-like / Ribonuclease H-like superfamily/Ribonuclease H / Ribonuclease H domain / RNase H type-1 domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribonuclease HI / :
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsAngkawidjaja, C. / Takano, K. / Kanaya, S.
CitationJournal: Plos One / Year: 2011
Title: Stabilization by fusion to the C-terminus of hyperthermophile Sulfolobus tokodaii RNase HI: a possibility of protein stabilization tag
Authors: Takano, K. / Okamoto, T. / Okada, J. / Tanaka, S. / Angkawidjaja, C. / Koga, Y. / Kanaya, S.
History
DepositionAug 10, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 uncharacterized protein ST0753
B: Putative uncharacterized protein ST0753


Theoretical massNumber of molelcules
Total (without water)32,4702
Polymers32,4702
Non-polymers00
Water4,576254
1
A: Putative uncharacterized protein ST0753


Theoretical massNumber of molelcules
Total (without water)16,2351
Polymers16,2351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative uncharacterized protein ST0753


Theoretical massNumber of molelcules
Total (without water)16,2351
Polymers16,2351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-7 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.975, 41.018, 43.534
Angle α, β, γ (deg.)89.72, 89.71, 86.76
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Putative uncharacterized protein ST0753 / ribonuclease HI / RNase HI


Mass: 16235.057 Da / Num. of mol.: 2 / Fragment: residues 1-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: str. 7 / Gene: ST0753 / Plasmid: pET25b+ / Production host: Escherichia coli (E. coli) / Strain (production host): MIC2067(DE3)
References: UniProt: Q973Z8, UniProt: F9VN79*PLUS, ribonuclease H
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 3000, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 4, 2009 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 32375 / % possible obs: 96.2 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 3.9 % / Rmerge(I) obs: 0.034 / Rsym value: 0.031 / Net I/σ(I): 37.21
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 6.14 / Num. unique all: 3175 / Rsym value: 0.193 / % possible all: 94.3

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Processing

Software
NameVersionClassification
BL38BSSdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EHG

2ehg


Resolution: 1.66→20.48 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.076 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R Free: 0.122
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25048 1639 5.1 %RANDOM
Rwork0.19714 ---
obs0.19996 30726 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.003 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.66→20.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 0 254 2498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222280
X-RAY DIFFRACTIONr_angle_refined_deg1.39123060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08323.61794
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.39215454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0571518
X-RAY DIFFRACTIONr_chiral_restr0.1150.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211654
X-RAY DIFFRACTIONr_mcbond_it1.8421.51396
X-RAY DIFFRACTIONr_mcangle_it3.03522250
X-RAY DIFFRACTIONr_scbond_it4.4363884
X-RAY DIFFRACTIONr_scangle_it7.2124.5810
LS refinement shellResolution: 1.657→1.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 104 -
Rwork0.284 2218 -
obs--94.89 %

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