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- PDB-1p9q: Structure of a hypothetical protein AF0491 from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 1p9q
TitleStructure of a hypothetical protein AF0491 from Archaeoglobus fulgidus
ComponentsHypothetical protein AF0491
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION
Function / homology
Function and homology information


cytosolic ribosome assembly
Similarity search - Function
SBDS protein C-terminal domain, subdomain 1 / Hypothetical 12.0 Kda Protein In Nam8-gar1 Intergenic Region; Chain: A; / Ribosome maturation protein SBDS, N-terminal domain / Ribosome maturation protein Sdo1/SBDS / Ribosome maturation protein SBDS, conserved site / Ribosome maturation protein SDO1/SBDS, central domain / Ribosome maturation protein Sdo1/SBDS, central domain superfamily / Ribosome maturation protein Sdo1/SBDS-like / Ribosome maturation protein SDO1/SBDS, C-terminal domain / SBDS protein, domain II ...SBDS protein C-terminal domain, subdomain 1 / Hypothetical 12.0 Kda Protein In Nam8-gar1 Intergenic Region; Chain: A; / Ribosome maturation protein SBDS, N-terminal domain / Ribosome maturation protein Sdo1/SBDS / Ribosome maturation protein SBDS, conserved site / Ribosome maturation protein SDO1/SBDS, central domain / Ribosome maturation protein Sdo1/SBDS, central domain superfamily / Ribosome maturation protein Sdo1/SBDS-like / Ribosome maturation protein SDO1/SBDS, C-terminal domain / SBDS protein, domain II / SBDS protein, C-terminal domain / Uncharacterized protein family UPF0023 signature. / Ribosome maturation protein SDO1/SBDS, N-terminal / Ribosome maturation protein SBDS, N-terminal domain superfamily / Shwachman-Bodian-Diamond syndrome (SBDS) protein / Alpha-Beta Plaits - #240 / EF-G domain III/V-like / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribosome maturation protein SDO1 homolog
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsSavchenko, A. / Evdokimova, E. / Skarina, T. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism.
Authors: Savchenko, A. / Krogan, N. / Cort, J.R. / Evdokimova, E. / Lew, J.M. / Yee, A.A. / Sanchez-Pulido, L. / Andrade, M.A. / Bochkarev, A. / Watson, J.D. / Kennedy, M.A. / Greenblatt, J. / ...Authors: Savchenko, A. / Krogan, N. / Cort, J.R. / Evdokimova, E. / Lew, J.M. / Yee, A.A. / Sanchez-Pulido, L. / Andrade, M.A. / Bochkarev, A. / Watson, J.D. / Kennedy, M.A. / Greenblatt, J. / Hughes, T. / Arrowsmith, C.H. / Rommens, J.M. / Edwards, A.M.
History
DepositionMay 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Hypothetical protein AF0491


Theoretical massNumber of molelcules
Total (without water)29,1781
Polymers29,1781
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.875, 44.254, 61.418
Angle α, β, γ (deg.)92.74, 118.02, 109.67
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Hypothetical protein AF0491


Mass: 29177.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF0491 / Plasmid: pET15 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29759
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.79 Å3/Da / Density % sol: 55.95 %
Description: F(+) AND F(-) WERE PROCESSED AND COUNTED AS INDEPENDENT REFLECTIONS (SCALE ANOMALOUS KEY IN SCALEPACK)
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Sodium acetate, PEG 3350, Ethylene Glycole, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 7.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931
DetectorType: SBC-2 / Detector: CCD / Date: Mar 17, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 35721 / % possible obs: 92.2 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.026 / Net I/σ(I): 23.2
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.166 / % possible all: 84.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SnB+ PHASES + SHARPphasing
ARP/wARP5.1 + CNS 1.1model building
HKL-2000data reduction
PHASESphasing
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD
Starting model: None

Resolution: 2→20 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: ARP/WARP 5.1 was also used for refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1752 9.8 %RANDOM
Rwork0.219 ---
all-19377 --
obs-17817 91.9 %-
Solvent computationSolvent model: flat model / Bsol: 55.7286 Å2 / ksol: 0.350447 e/Å3
Displacement parametersBiso mean: 50.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.58 Å26.28 Å27.18 Å2
2--4.05 Å214.82 Å2
3---0.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 0 145 1979
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.633
X-RAY DIFFRACTIONc_mcangle_it5.024
X-RAY DIFFRACTIONc_scbond_it5.214
X-RAY DIFFRACTIONc_scangle_it7.215.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 215 8.4 %
Rwork0.376 2337 -
obs--79.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMprotein.top
X-RAY DIFFRACTION2WATER_REP.PARAMwater.top

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