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- PDB-2cxh: Crystal structure of probable ribosomal biogenesis protein from A... -

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Basic information

Entry
Database: PDB / ID: 2cxh
TitleCrystal structure of probable ribosomal biogenesis protein from Aeropyrum pernix K1
ComponentsProbable brix-domain ribosomal biogenesis protein
KeywordsRNA BINDING PROTEIN / BRIX domain / 18S rRNA / IMP4 / U3 snoRNP / ribosomal biogenesis / RNA-binding / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


rRNA processing / rRNA binding
Similarity search - Function
Probable Brix domain-containing ribosomal biogenesis protein / Brix domain / Brix domain / Brix domain profile. / Brix / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable Brix domain-containing ribosomal biogenesis protein
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKawazoe, M. / Takemoto, C. / Hanawa-Suetsugu, K. / Kaminishi, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of probable ribosomal biogenesis protein from Aeropyrum pernix K1
Authors: Kawazoe, M. / Takemoto, C. / Hanawa-Suetsugu, K. / Kaminishi, T. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 29, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable brix-domain ribosomal biogenesis protein


Theoretical massNumber of molelcules
Total (without water)23,7751
Polymers23,7751
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.171, 47.364, 124.675
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 Probable brix-domain ribosomal biogenesis protein


Mass: 23774.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: APE1443 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) pRARE / References: UniProt: Q9YC08
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26692 Å3/Da / Density % sol: 45.741364 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.01M Tris-HCl pH 8.0, 0.15M NaCl, 0.001M DTT, 0.05M tri-sodium citrate pH 5.6, 10% v/v 2-propanol, 10% w/v polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 15, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.697→37.796 Å / Num. obs: 22973 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 8.36835 % / Biso Wilson estimate: 11 Å2 / Rsym value: 0.09 / Net I/σ(I): 23.616
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 22973 / Rsym value: 0.608 / % possible all: 95.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→37.71 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1210188.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.209 920 4.8 %RANDOM
Rwork0.184 ---
obs0.184 19230 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.244 Å2 / ksol: 0.36566 e/Å3
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å20 Å2
2--3.25 Å20 Å2
3----1.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 0 150 1540
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.382
X-RAY DIFFRACTIONc_scangle_it3.592.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.214 146 4.5 %
Rwork0.203 3066 -
obs--95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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