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- PDB-2ef7: Crystal structure of ST2348, a hypothetical protein with CBS doma... -

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Basic information

Entry
Database: PDB / ID: 2ef7
TitleCrystal structure of ST2348, a hypothetical protein with CBS domains from Sulfolobus tokodaii strain7
ComponentsHypothetical protein ST2348
KeywordsOXIDOREDUCTASE / CBS-domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsAgari, Y. / Karthe, P. / Kumarevel, T. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Crystal structure of ST2348, a CBS domain protein, from hyperthermophilic archaeon Sulfolobus tokodaii
Authors: Ragunathan, P. / Kumarevel, T. / Agari, Y. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Ponnuraj, K.
History
DepositionFeb 21, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein ST2348
B: Hypothetical protein ST2348


Theoretical massNumber of molelcules
Total (without water)30,2932
Polymers30,2932
Non-polymers00
Water2,414134
1
A: Hypothetical protein ST2348
B: Hypothetical protein ST2348

A: Hypothetical protein ST2348
B: Hypothetical protein ST2348


Theoretical massNumber of molelcules
Total (without water)60,5864
Polymers60,5864
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6500 Å2
ΔGint-41 kcal/mol
Surface area24360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)51.420, 135.272, 41.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hypothetical protein ST2348


Mass: 15146.499 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): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: Q96Y20
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 160mM ammonium chloride, 16%(w/v) polyethylene glycol 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97897, 0.9, 0.97929
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 17, 2006
RadiationMonochromator: Si Double Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978971
20.91
30.979291
ReflectionResolution: 2.1→40 Å / Num. all: 17492 / Num. obs: 17492 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 32.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.89 / Num. unique all: 1682 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→39.44 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1397823.16 / 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
Rfree0.26 1734 9.9 %RANDOM
Rwork0.216 ---
all0.22 17453 --
obs0.216 17453 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.1767 Å2 / ksol: 0.368075 e/Å3
Displacement parametersBiso mean: 38.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---10.6 Å20 Å2
3---10.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1950 0 0 134 2084
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it3.331.5
X-RAY DIFFRACTIONc_mcangle_it4.292
X-RAY DIFFRACTIONc_scbond_it6.082
X-RAY DIFFRACTIONc_scangle_it8.262.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 290 10.3 %
Rwork0.245 2516 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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