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- PDB-1v77: Crystal structure of the PH1877 protein -

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Basic information

Entry
Database: PDB / ID: 1v77
TitleCrystal structure of the PH1877 protein
Componentshypothetical protein PH1877
KeywordsRNA BINDING PROTEIN / RNase P protein / TIM-barrel
Function / homology
Function and homology information


ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / cytoplasm
Similarity search - Function
Ribonuclease P, protein component 3, archaeal / RNase P subunit p30 / RNase P subunit p30 / Polymerase/histidinol phosphatase-like / Metal-dependent hydrolases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Ribonuclease P protein component 3
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsTakagi, H. / Numata, T. / Kakuta, Y. / Kimura, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Crystal structure of the ribonuclease P protein Ph1877p from hyperthermophilic archaeon Pyrococcus horikoshii OT3
Authors: Takagi, H. / Watanabe, M. / Kakuta, Y. / Kamachi, R. / Numata, T. / Tanaka, I. / Kimura, M.
History
DepositionDec 12, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Dec 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: hypothetical protein PH1877


Theoretical massNumber of molelcules
Total (without water)24,7341
Polymers24,7341
Non-polymers00
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.853, 46.853, 218.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein hypothetical protein PH1877 / PH1877p


Mass: 24734.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1877 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami(DE3) / References: UniProt: O59543, ribonuclease P
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.26 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22.5% PEG 6000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9792, 0.9795, 0.9870
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 7, 2003
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97951
30.9871
ReflectionResolution: 1.8→50 Å / Num. all: 42142 / Num. obs: 42142 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 22.2 Å2 / Rsym value: 0.107 / Net I/σ(I): 13.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 5.9 / Num. unique all: 42412 / Rsym value: 0.204 / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→30.16 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 893016.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2677 2052 5 %RANDOM
Rwork0.2296 ---
obs0.2296 41080 95.3 %-
all-41080 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 13.506 Å2 / ksol: 1.51056 e/Å3
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å-0.32 Å
Refinement stepCycle: LAST / Resolution: 1.8→30.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 0 225 1894
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it02
X-RAY DIFFRACTIONc_scangle_it02.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.543 317 5 %
Rwork0.554 5970 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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