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- PDB-2pd2: Crystal structure of (ST0148) conserved hypothetical from Sulfolo... -

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Basic information

Entry
Database: PDB / ID: 2pd2
TitleCrystal structure of (ST0148) conserved hypothetical from Sulfolobus Tokodaii Strain7
ComponentsHypothetical protein ST0148
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologySulphur relay, DsrE/F-like / DsrE/DsrF-like family / DsrEFH-like / DsrEFH-like / Hypothetical Protein Ychn; Chain: A, / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsJeyakanthan, J. / Kanaujia, S.P. / Rafi, Z.A. / Sekar, K. / Agari, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of (ST0148) conserved hypothetical from Sulfolobus Tokodaii Strain7
Authors: Jeyakanthan, J. / Kanaujia, S.P. / Rafi, Z.A. / Sekar, K. / Agari, Y. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y.
History
DepositionMar 31, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein ST0148
B: Hypothetical protein ST0148


Theoretical massNumber of molelcules
Total (without water)24,2202
Polymers24,2202
Non-polymers00
Water2,738152
1
A: Hypothetical protein ST0148

A: Hypothetical protein ST0148

A: Hypothetical protein ST0148


Theoretical massNumber of molelcules
Total (without water)36,3303
Polymers36,3303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
2
B: Hypothetical protein ST0148

B: Hypothetical protein ST0148

B: Hypothetical protein ST0148


Theoretical massNumber of molelcules
Total (without water)36,3303
Polymers36,3303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Unit cell
Length a, b, c (Å)112.272, 112.272, 112.272
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Hypothetical protein ST0148


Mass: 12110.106 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 CONDON PLUS (DE3)-RIL / References: UniProt: Q976P3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 293 K / Method: oil-batch / pH: 8.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1M Tris-HCl, 30% PEG 4000, pH 8.5, OIL-BATCH, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 19, 2006 / Details: RH COATED BENT-CYRINDRICAL MIRROR
RadiationMonochromator: SI-1 1 1 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→40 Å / Num. all: 14722 / Num. obs: 14722 / % possible obs: 98.3 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.066
Reflection shellResolution: 2.06→2.12 Å / Rmerge(I) obs: 0.2 / Num. unique all: 1228 / Rsym value: 0.2 / % possible all: 82.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L1S

1l1s


Resolution: 2.06→35.5 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2098316.25 / 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
Rfree0.236 1482 10.2 %RANDOM
Rwork0.186 ---
obs0.186 14597 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.4387 Å2 / ksol: 0.341476 e/Å3
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2.06→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 0 152 1852
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.06→2.15 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.271 180 10.1 %
Rwork0.189 1608 -
obs--97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION5water_rep.paramwater_protin.top

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