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- PDB-1woz: Crystal structure of uncharacterized protein ST1454 from Sulfolob... -

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Basic information

Entry
Database: PDB / ID: 1woz
TitleCrystal structure of uncharacterized protein ST1454 from Sulfolobus tokodaii
Components177aa long conserved hypothetical protein (ST1454)
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION
Function / homology
Function and homology information


corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / ATP binding
Similarity search - Function
Hypothetical Protein Ta1238; Chain: A; / Cobalamin adenosyltransferase-like / Cobalamin adenosyltransferase-like / Corrinoid adenosyltransferase, PduO-type / Cobalamin adenosyltransferase / Cobalamin adenosyltransferase-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-POG / PduO-type ATP--cob(I)alamin adenosyltransferase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.94 Å
AuthorsSasaki, T. / Tanaka, Y. / Yasutake, Y. / Yao, M. / Tanaka, I. / Tsumoto, K. / Kumagai, I.
CitationJournal: To be Published
Title: Crystal structure of the uncharacterized protein ST1454 from Sulfolobus tokodaii.
Authors: Sasaki, T. / Tanaka, Y. / Yasutake, Y. / Yao, M. / Tanaka, I. / Tsumoto, K. / Kumagai, I.
History
DepositionAug 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 177aa long conserved hypothetical protein (ST1454)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0332
Polymers20,6081
Non-polymers4251
Water1,78399
1
A: 177aa long conserved hypothetical protein (ST1454)
hetero molecules

A: 177aa long conserved hypothetical protein (ST1454)
hetero molecules

A: 177aa long conserved hypothetical protein (ST1454)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0986
Polymers61,8243
Non-polymers1,2743
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)84.670, 84.670, 84.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -z+1/2, -x, y+1/2 and -y, z-1/2, -x+1/2.

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Components

#1: Protein 177aa long conserved hypothetical protein (ST1454)


Mass: 20608.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: ST1454 / Plasmid: pET20B / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q970Z7
#2: Chemical ChemComp-POG / (20S)-2,5,8,11,14,17-HEXAMETHYL-3,6,9,12,15,18-HEXAOXAHENICOSANE-1,20-DIOL / POLYPROPYLENE GLYCOL, HEPTAPROPYLENE GLYCOL


Mass: 424.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.48 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: HEPES buffer, Ammonium sulfate, PEG400, Polypropylene glycol 400, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.97967, 0.97997, 0.9000
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 17, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979671
20.979971
30.91
ReflectionResolution: 1.94→50 Å / Num. all: 15276 / Num. obs: 15276 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 19.2 % / Biso Wilson estimate: 36.7 Å2 / Rsym value: 0.08 / Net I/σ(I): 9
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 19.7 % / Num. unique all: 1502 / Rsym value: 0.399 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.94→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1537 -RANDOM
Rwork0.1739 ---
all-15249 --
obs-15249 100 %-
Displacement parametersBiso mean: 26.587 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å-0.03 Å
Refinement stepCycle: LAST / Resolution: 1.94→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1299 0 6 99 1404
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011622
X-RAY DIFFRACTIONc_angle_deg1.5048
X-RAY DIFFRACTIONc_dihedral_angle_d19.50221
X-RAY DIFFRACTIONc_improper_angle_d1.77985
X-RAY DIFFRACTIONc_mcangle_it1.772
X-RAY DIFFRACTIONc_mcbond_it1.214
X-RAY DIFFRACTIONc_scangle_it3.293
X-RAY DIFFRACTIONc_scbond_it2.223
LS refinement shellResolution: 1.94→2.01 Å
RfactorNum. reflection% reflection
Rfree0.2232 166 -
Rwork0.1668 --
obs-1498 100 %

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