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- PDB-3asm: Crystal structure of Q54A mutant protein of Bst-RNase HIII -

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Basic information

Entry
Database: PDB / ID: 3asm
TitleCrystal structure of Q54A mutant protein of Bst-RNase HIII
ComponentsRibonuclease HIII
KeywordsHYDROLASE / RNase / DNA/RNA binding
Function / homology
Function and homology information


RNA catabolic process / ribonuclease H / RNA-DNA hybrid ribonuclease activity / magnesium ion binding / RNA binding / cytoplasm
Similarity search - Function
Domain of unknown function (DUF3378) / Ribonuclease HIII, N-terminal / Ribonuclease HIII / Ribonuclease (RNase) H type-2 domain profile. / Ribonuclease HII/HIII / Ribonuclease HII/HIII domain / Ribonuclease HII / TATA-Binding Protein / TATA-Binding Protein / TBP domain superfamily ...Domain of unknown function (DUF3378) / Ribonuclease HIII, N-terminal / Ribonuclease HIII / Ribonuclease (RNase) H type-2 domain profile. / Ribonuclease HII/HIII / Ribonuclease HII/HIII domain / Ribonuclease HII / TATA-Binding Protein / TATA-Binding Protein / TBP domain superfamily / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsAngkawidjaja, C. / Kanaya, S.
CitationJournal: Febs Lett. / Year: 2011
Title: Identification of the substrate binding site in the N-terminal TBP-like domain of RNase H3.
Authors: Miyashita, S. / Tadokoro, T. / Angkawidjaja, C. / You, D.-J. / Koga, Y. / Takano, K. / Kanaya, S.
History
DepositionDec 16, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Nov 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease HIII


Theoretical massNumber of molelcules
Total (without water)33,8161
Polymers33,8161
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.249, 109.106, 48.329
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ribonuclease HIII / RNase HIII


Mass: 33815.895 Da / Num. of mol.: 1 / Mutation: Q54A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pET25b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Mic2067(de3) / References: UniProt: Q6L6Q4, ribonuclease H
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.085M Tris-HCl pH 8.5, 0.17M lithium sulfate, 25.5% PEG 4000, 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 14, 2008 / Details: mirrors
RadiationMonochromator: mirros / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 11445 / % possible obs: 99.9 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 6.9 % / Rmerge(I) obs: 0.106 / Rsym value: 0.086 / Net I/σ(I): 18.5 / Num. measured all: 240534
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.33 / Num. unique all: 1102 / Rsym value: 0.355 / % possible all: 98.9

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Processing

Software
NameVersionClassification
BL38BSSdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D0A

2d0a


Resolution: 2.603→44.19 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.81 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R Free: 0.29
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23262 546 4.8 %RANDOM
Rwork0.20364 ---
obs0.20498 10867 99.89 %-
all-11413 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.873 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.603→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 0 58 2417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222401
X-RAY DIFFRACTIONr_angle_refined_deg0.9251.9653252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4485307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51123.301103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.9515414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9691521
X-RAY DIFFRACTIONr_chiral_restr0.0760.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211804
X-RAY DIFFRACTIONr_mcbond_it1.3011.51537
X-RAY DIFFRACTIONr_mcangle_it2.3822455
X-RAY DIFFRACTIONr_scbond_it3.8173864
X-RAY DIFFRACTIONr_scangle_it5.8134.5797
LS refinement shellResolution: 2.603→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 45 -
Rwork0.293 759 -
obs--98.53 %

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