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- PDB-1xg8: Crystal Structure of Protein of Unknown Function SA0789 from Stap... -

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Basic information

Entry
Database: PDB / ID: 1xg8
TitleCrystal Structure of Protein of Unknown Function SA0789 from Staphylococcus aureus
Componentshypothetical protein SA0798
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initative / MCSG / Staphylococcus aureus / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


Hypothetical protein sa0798. / Protein of unknown function DUF1462 / YuzD-like superfamily / Protein of unknown function (DUF1462) / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Disulfide oxidoreductase / Uncharacterized protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsRotella, F.J. / Zhang, R.G. / Kim, Y. / Quartey, P. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The 2.1A crystal structure of hypothetical protein SA0798 from Staphylococcus aureus
Authors: Rotella, F.J. / Zhang, R.G. / Kim, Y. / Quartey, P. / Collart, F. / Joachimiak, A.
History
DepositionSep 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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 SA0798


Theoretical massNumber of molelcules
Total (without water)13,0391
Polymers13,0391
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.174, 41.174, 127.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsthe biological assembly is monomer

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Components

#1: Protein hypothetical protein SA0798


Mass: 13038.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria)
Species: Staphylococcus aureus / Strain: subsp. aureus N315 / Gene: GI:1123613 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7A6J8, UniProt: A0A0H3JTK4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.35 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 5
Details: ammonium sulfate, citrate buffer, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979569, 0.979706, 0.964107
DetectorType: SBC-2 / Detector: CCD / Date: Mar 16, 2004 / Details: vertical-focusing mirror
RadiationMonochromator: Si-111 double-crystal channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9795691
20.9797061
30.9641071
ReflectionResolution: 2.1→50 Å / Num. all: 12274 / Num. obs: 11783 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 18.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 1.73 / Num. unique all: 1235 / % possible all: 71.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.6 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 226196.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 551 5 %RANDOM
Rwork0.229 ---
obs0.229 11083 90.6 %-
all-12233 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.2014 Å2 / ksol: 0.39592 e/Å3
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.49 Å20 Å20 Å2
2--2.49 Å20 Å2
3----4.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 0 0 41 933
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.377 71 5.4 %
Rwork0.34 1247 -
obs--64.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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