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- PDB-2ejx: Crystal structure of the hypothetical protein STK_08120 from Sulf... -

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Basic information

Entry
Database: PDB / ID: 2ejx
TitleCrystal structure of the hypothetical protein STK_08120 from Sulfolobus tokodaii
ComponentsSTK_08120
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ARCAEA / STK_08120 / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homologyProtein of unknown function DUF3211 / STK_08120-like / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / DUF3211 domain-containing protein
Function and homology information
Biological speciesSulfolobus tokodaii str. 7 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å
AuthorsMiyakawa, T. / Miyazono, K. / Sawano, Y. / Hatano, K. / Nagata, K. / Tanokura, M.
CitationJournal: J.Bacteriol. / Year: 2013
Title: A thermoacidophile-specific protein family, DUF3211, functions as a fatty acid carrier with novel binding mode
Authors: Miyakawa, T. / Sawano, Y. / Miyazono, K. / Miyauchi, Y. / Hatano, K. / Tanokura, M.
History
DepositionMar 21, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Nov 6, 2013Group: Database references
Revision 1.4Mar 13, 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: STK_08120


Theoretical massNumber of molelcules
Total (without water)16,0161
Polymers16,0161
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: STK_08120

A: STK_08120


Theoretical massNumber of molelcules
Total (without water)32,0312
Polymers32,0312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1260 Å2
ΔGint-6.4 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.887, 70.446, 35.230
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 STK_08120


Mass: 16015.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii str. 7 (archaea) / Species: Sulfolobus tokodaii / Strain: strain 7 / Gene: STK_08120 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q973T5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 15% PEG4000, 20% isopropanol, 100mM MES, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SYNCHROTRONPhoton Factory AR-NW12A20.97924
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDOct 29, 2006
ADSC QUANTUM 2102CCDNov 12, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979241
ReflectionResolution: 1.79→50 Å / Num. obs: 13524 / % possible obs: 97.8 % / Redundancy: 5.5 % / Rsym value: 0.072 / Net I/σ(I): 43.9
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 6 % / Mean I/σ(I) obs: 10.8 / Rsym value: 0.255 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.79→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.604 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26171 652 4.9 %RANDOM
Rwork0.22035 ---
obs0.22246 12526 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.835 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.79→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 0 102 1192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221107
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9841489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5025133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57824.42352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41515219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.168158
X-RAY DIFFRACTIONr_chiral_restr0.1090.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02815
X-RAY DIFFRACTIONr_nbd_refined0.2050.2511
X-RAY DIFFRACTIONr_nbtor_refined0.310.2778
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.27
X-RAY DIFFRACTIONr_mcbond_it1.0971.5689
X-RAY DIFFRACTIONr_mcangle_it1.76221092
X-RAY DIFFRACTIONr_scbond_it2.9393463
X-RAY DIFFRACTIONr_scangle_it4.4854.5397
LS refinement shellResolution: 1.788→1.834 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 51 -
Rwork0.266 885 -
obs-885 94.55 %

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