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- PDB-2rbg: Crystal structure of hypothetical protein(ST0493) from sulfolobus... -

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Basic information

Entry
Database: PDB / ID: 2rbg
TitleCrystal structure of hypothetical protein(ST0493) from sulfolobus tokodaii
ComponentsPutative uncharacterized protein ST0493
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyRossmann fold - #11100 / Domain of unknown function DUF5751 / Family of unknown function (DUF5751) / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DUF5751 domain-containing protein
Function and homology information
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJeyakanthan, J. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein(ST0493) from sulfolobus tokodaii
Authors: Jeyakanthan, J. / Kuramitsu, S. / Yokoyama, S.
History
DepositionSep 19, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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_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_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

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Assembly

Deposited unit
A: Putative uncharacterized protein ST0493
B: Putative uncharacterized protein ST0493
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0203
Polymers29,9242
Non-polymers961
Water5,693316
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative uncharacterized protein ST0493


Theoretical massNumber of molelcules
Total (without water)14,9621
Polymers14,9621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Putative uncharacterized protein ST0493
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0582
Polymers14,9621
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.444, 65.184, 49.604
Angle α, β, γ (deg.)90.00, 98.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein ST0493


Mass: 14961.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: Strain 7 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta834(DE3) / References: UniProt: Q975B5
#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.: 316 / 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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 30% PEG 4K, 0.2M Ammonium Sulfate, pH 7.5, MICROBATCH, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97899, 0.9, 0.97931
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2007 / Details: RH COATED BENT-CYRINDRICAL MIRROR
RadiationMonochromator: SI-1 1 1 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978991
20.91
30.979311
ReflectionResolution: 1.75→50 Å / Num. obs: 25105 / % possible obs: 99.6 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.063
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.143 / Num. unique all: 2433 / Rsym value: 0.133 / % possible all: 96.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→33.49 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2067291.84 / 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
Rfree0.196 1216 4.9 %RANDOM
Rwork0.173 ---
obs0.173 25029 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2041 Å2 / ksol: 0.371373 e/Å3
Displacement parametersBiso mean: 16.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å20 Å2-1.31 Å2
2---1 Å20 Å2
3----1.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.75→33.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 5 316 2381
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 1.75→1.83 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.242 156 5.1 %
Rwork0.198 2906 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ligand.paramligand.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION5water_rep.paramwater_protin.top

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