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- PDB-1lxj: X-RAY STRUCTURE OF YBL001c NORTHEAST STRUCTURAL GENOMICS (NESG) C... -

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Basic information

Entry
Database: PDB / ID: 1lxj
TitleX-RAY STRUCTURE OF YBL001c NORTHEAST STRUCTURAL GENOMICS (NESG) CONSORTIUM TARGET YTYst72
ComponentsHYPOTHETICAL 11.5KDA PROTEIN IN HTB2-NTH2 INTERGENIC REGION
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical protein / HTB2-NTH2 intergenic region / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


nucleus / cytoplasm / cytosol
Similarity search - Function
Thiamine-binding protein / Thiamine-binding protein / Alpha-Beta Plaits - #930 / MTH1187/YkoF-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
UPF0045 protein ECM15
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsTao, X. / Khayat, R. / Christendat, D. / Savchenko, A. / Xu, X. / Edwards, A. / Arrowsmith, C.H. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2003
Title: CRYSTAL STRUCTURES OF MTH1187 AND ITS YEAST ORTHOLOG YBL001C
Authors: Tao, X. / Khayat, R. / Christendat, D. / Savchenko, A. / Xu, X. / Goldsmith-Fischman, S. / Honig, B. / Edwards, A. / Arrowsmith, C.H. / Tong, L.
History
DepositionJun 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL 11.5KDA PROTEIN IN HTB2-NTH2 INTERGENIC REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7732
Polymers11,6771
Non-polymers961
Water4,017223
1
A: HYPOTHETICAL 11.5KDA PROTEIN IN HTB2-NTH2 INTERGENIC REGION
hetero molecules

A: HYPOTHETICAL 11.5KDA PROTEIN IN HTB2-NTH2 INTERGENIC REGION
hetero molecules

A: HYPOTHETICAL 11.5KDA PROTEIN IN HTB2-NTH2 INTERGENIC REGION
hetero molecules

A: HYPOTHETICAL 11.5KDA PROTEIN IN HTB2-NTH2 INTERGENIC REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0928
Polymers46,7084
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_765-x+2,-y+1,z1
crystal symmetry operation16_665-y+3/2,-x+3/2,-z+1/21
Buried area12970 Å2
ΔGint-140 kcal/mol
Surface area15890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.380, 67.380, 133.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein HYPOTHETICAL 11.5KDA PROTEIN IN HTB2-NTH2 INTERGENIC REGION / YBL001C


Mass: 11676.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P35195
#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.: 223 / 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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium Sulfate, 2-METHYL-2,4-PENTANEDIOL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mMHEPES1drop
2500 mM1dropNaCl
320 mg/mlprotein1drop
40.1 MTris1reservoirpH8.5
52 Mammonium sulfate1reservoir
612 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97895 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 4, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 12726 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.5 Å2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 85.7
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. measured all: 141589 / Rmerge(I) obs: 0.096

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 4329413.23 / Data cutoff high rms absF: 4329413.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 900 7.2 %RANDOM
Rwork0.211 ---
all-14671 --
obs-12581 85.7 %-
Solvent computationBsol: 52.0701 Å2 / ksol: 0.351892 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--0.9 Å20 Å2
3----1.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms807 0 5 223 1035
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.005
X-RAY DIFFRACTIONo_angle_deg1.1
X-RAY DIFFRACTIONo_dihedral_angle_d23.2
X-RAY DIFFRACTIONo_improper_angle_d0.78
X-RAY DIFFRACTIONo_mcbond_it1.321.5
X-RAY DIFFRACTIONo_mcangle_it2.062
X-RAY DIFFRACTIONo_scbond_it2.392
X-RAY DIFFRACTIONo_scangle_it3.292.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 119 6.9 %
Rwork0.278 1606 -
obs-1725 72.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMTOP.SO4
X-RAY DIFFRACTION3PARAM.SO4
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Num. reflection obs: 13776
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg23.2
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg0.78

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