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- PDB-1yoz: Predicted coding region AF0941 from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 1yoz
TitlePredicted coding region AF0941 from Archaeoglobus fulgidus
ComponentsHypothetical protein AF0941
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / AF0941 / APC5573 / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homologyAF0941-like / Uncharacterised domain AF0941 / AF0941-like superfamily / AF0941-like / Hypothetical protein af0941 / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein AF_0941
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLunin, V.V. / Zhang, R. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of predicted coding region AF0941 from Archaeoglobus fulgidus
Authors: Lunin, V.V. / Botchkareva, E. / Zhang, R. / Joachimiak, A. / Edwards, A.M. / Savchenko, A.
History
DepositionJan 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 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
A: Hypothetical protein AF0941
B: Hypothetical protein AF0941


Theoretical massNumber of molelcules
Total (without water)27,5802
Polymers27,5802
Non-polymers00
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.492, 72.492, 165.271
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-196-

HOH

21B-201-

HOH

31B-209-

HOH

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Components

#1: Protein Hypothetical protein AF0941


Mass: 13789.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: MODIFIED PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O29321
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.5M (NH4)2SO4, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.97946 / Wavelength: 0.97946 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.95→63 Å / Num. all: 17895 / Num. obs: 17895 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.049 / Net I/σ(I): 56.67
Reflection shellResolution: 1.95→2.02 Å / Mean I/σ(I) obs: 8.1 / Rsym value: 0.383 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2→62.75 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 5.723 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30031 915 5.1 %RANDOM
Rwork0.23091 ---
obs0.23435 16980 98.63 %-
all-17023 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.995 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.34 Å20 Å2
2--0.67 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 2→62.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 0 199 2108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221935
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.9842581
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6135226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22125.049103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.51815405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5391512
X-RAY DIFFRACTIONr_chiral_restr0.1190.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021427
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.21026
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21356
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2181
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5821.51200
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85221828
X-RAY DIFFRACTIONr_scbond_it3.0023848
X-RAY DIFFRACTIONr_scangle_it4.4874.5753
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 79 -
Rwork0.266 1222 -
obs--99.77 %

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