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- PDB-3af6: The crystal structure of an archaeal CPSF subunit, PH1404 from Py... -

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Basic information

Entry
Database: PDB / ID: 3af6
TitleThe crystal structure of an archaeal CPSF subunit, PH1404 from Pyrococcus horikoshii complexed with RNA-analog
Components
  • 5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3'
  • Putative uncharacterized protein PH1404
KeywordsHYDROLASE/RNA / archaeal CPSF / beta-CASP family / KH domain / ribonuclease / metallo-beta-lactamase superfamily / Pyrococcus horikoshii / archaea / RNA-analog / HYDROLASE-RNA complex
Function / homology
Function and homology information


RNA binding / metal ion binding
Similarity search - Function
GMP Synthetase; Chain A, domain 3 - #230 / Transcription termination factor CPSF1, archaea / KH domain, archaeal / KH domain / Rossmann fold - #10890 / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain ...GMP Synthetase; Chain A, domain 3 - #230 / Transcription termination factor CPSF1, archaea / KH domain, archaeal / KH domain / Rossmann fold - #10890 / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / K Homology domain / K homology RNA-binding domain / K homology domain superfamily, prokaryotic type / 4-Layer Sandwich / K homology domain-like, alpha/beta / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Uncharacterized protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNishida, Y. / Ishikawa, H. / Nakagawa, N. / Masui, R. / Kuramitsu, S.
CitationJournal: Proteins / Year: 2010
Title: Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii
Authors: Nishida, Y. / Ishikawa, H. / Baba, S. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionFeb 24, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein PH1404
B: 5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3'
C: 5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,44410
Polymers77,8323
Non-polymers6117
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.438, 86.438, 237.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-35-

HOH

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Components

#1: Protein Putative uncharacterized protein PH1404


Mass: 74055.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1404 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O50112
#2: RNA chain 5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3'


Mass: 1888.433 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA-analog
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 0.1M sodium acetate, 0.1M sodium chloride, 8% (v/v) PEG 6000, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 27, 2008
RadiationMonochromator: Si double crystal monochromator / 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: 52847 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 59.9 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 27.12
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.06 / Num. unique all: 5236 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AF5

3af5


Resolution: 2.6→42.59 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 97464.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED; THE FRIEDEL PAIRS WERE USED FOR phasing.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 5026 9.9 %RANDOM
Rwork0.22 ---
obs0.22 50924 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.1113 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 66 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2--1.54 Å20 Å2
3----3.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.6→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5099 106 27 37 5269
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it3.032.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 815 10.5 %
Rwork0.306 6977 -
obs-6977 88.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep_PH1404.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ligand.paramligand.top
X-RAY DIFFRACTION5dna-rna_rep_ssU.paramdna-rna_ssU.top

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