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- PDB-1uc2: Hypothetical Extein Protein of PH1602 from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 1uc2
TitleHypothetical Extein Protein of PH1602 from Pyrococcus horikoshii
Componentshypothetical protein PH1602
KeywordsLIGASE / Structural genomics
Function / homology
Function and homology information


RNA splicing, via endonucleolytic cleavage and ligation / 3'-phosphate/5'-hydroxy nucleic acid ligase / : / tRNA-splicing ligase complex / GMP binding / RNA ligase (ATP) activity / intein-mediated protein splicing / intron homing / manganese ion binding / endonuclease activity ...RNA splicing, via endonucleolytic cleavage and ligation / 3'-phosphate/5'-hydroxy nucleic acid ligase / : / tRNA-splicing ligase complex / GMP binding / RNA ligase (ATP) activity / intein-mediated protein splicing / intron homing / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds / GTP binding / DNA binding
Similarity search - Function
tRNA-splicing ligase RtcB / tRNA-splicing ligase RtcB / RNA-splicing ligase, RtcB / tRNA-splicing ligase RtcB-like superfamily / tRNA-splicing ligase RtcB / LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. ...tRNA-splicing ligase RtcB / tRNA-splicing ligase RtcB / RNA-splicing ligase, RtcB / tRNA-splicing ligase RtcB-like superfamily / tRNA-splicing ligase RtcB / LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
sucrose / tRNA-splicing ligase RtcB
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsOkada, C. / Maegawa, Y. / Yao, M. / Tanaka, I.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of an RtcB homolog protein (PH1602-extein protein) from Pyrococcus horikoshii reveals a novel fold
Authors: Okada, C. / Maegawa, Y. / Yao, M. / Tanaka, I.
History
DepositionApr 8, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 14, 2012Group: Structure summary
Revision 1.4Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _software.classification / _software.name
Revision 1.5Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein PH1602
B: hypothetical protein PH1602
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,71413
Polymers107,1652
Non-polymers1,54911
Water15,691871
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.251, 137.586, 148.500
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 hypothetical protein PH1602 / PH1602


Mass: 53582.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1602_extein / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O59245
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 871 / 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: 3.879 Å3/Da / Density % sol: 68.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Sodium Chloride, ammonium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.15→39.39 Å / Num. all: 108175 / Num. obs: 90861 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 5.3 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.077 / Net I/σ(I): 8.5
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.4 / Num. unique all: 13038 / Rsym value: 0.305 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
HKL-2000data collection
SCALAdata scaling
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNSrefinement
HKL-2000data reduction
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 8944 9.9 %RANDAM
Rwork0.168 ---
all-89812 --
obs-89812 99.7 %-
Solvent computationBsol: 66.86 Å2 / ksol: 0.424 e/Å3
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.67 Å20 Å20 Å2
2---3.681 Å20 Å2
3---0.011 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7518 0 91 871 8480
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5983
X-RAY DIFFRACTIONc_dihedral_angle_d23.741
X-RAY DIFFRACTIONc_improper_angle_d1.0045
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.62
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it3.92.5
LS refinement shellResolution: 2.15→2.23 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.247 883 10 %
Rwork0.211 7945 -
obs-8828 99.1 %

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