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- PDB-1kk9: CRYSTAL STRUCTURE OF E. COLI YCIO -

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Basic information

Entry
Database: PDB / ID: 1kk9
TitleCRYSTAL STRUCTURE OF E. COLI YCIO
Componentsprobable translation factor yciO
KeywordsUNKNOWN FUNCTION / alpha/beta open twisted sheet / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics
Function / homology
Function and homology information


double-stranded RNA binding / cytosol
Similarity search - Function
: / Threonylcarbamoyl-AMP synthase-like domain / Telomere recombination / YrdC-like domain profile. / DHBP synthase / DHBP synthase / DHBP synthase RibB-like alpha/beta domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein YciO / Uncharacterized protein YciO
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJia, J. / Lunin, V.V. / Sauve, V. / Huang, L.-W. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
Citation
Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2002
Title: Crystal structure of the YciO protein from Escherichia coli
Authors: Jia, J. / Lunin, V.V. / Sauve, V. / Huang, L.-W. / Matte, A. / Cygler, M.
#1: Journal: Protein Sci. / Year: 2000
Title: The structure of the Yrdc gene product from E.coli
Authors: Teplova, M. / Tereshko, R. / Sanishvili, A. / Joachimiak, A. / Bushueva, T. / Anderson, W.F. / Egli, M.
History
DepositionDec 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 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 / struct_site
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 / _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: probable translation factor yciO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2872
Polymers25,1911
Non-polymers961
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.400, 68.770, 94.770
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 translation factor yciO


Mass: 25190.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ycio / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P45847, UniProt: P0AFR4*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.47 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, MES, magnesium acetate, ethylene glycol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
220 mMTris1droppH7.5
340 mMammonium sulfate1drop
460 mM1dropNH4Ac
55 mM2-mercaptoethanol1drop
610 %(w/v)PEG33501reservoir
70.1 MMES1reservoirpH6.5
80.1 M1reservoirMgAc2
95 %(v/v)ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.97921,0.97942,0.95369
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.979421
30.953691
ReflectionResolution: 2.1→50 Å / Num. all: 19133 / Num. obs: 18736 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 10.7 % / Rsym value: 0.068 / Net I/σ(I): 10.4
Reflection shellResolution: 2.1→2.18 Å / Num. unique all: 1869 / Rsym value: 0.422 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 19133 / Num. measured all: 205748 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.422

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Processing

Software
NameVersionClassification
Adxvdata processing
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 911 4.8 %random
Rwork0.213 ---
obs-18731 98.1 %-
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 5 126 1759
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.46
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.005
X-RAY DIFFRACTIONo_angle_deg1.3

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