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- PDB-3o12: The crystal structure of a functionally unknown protein from Sacc... -

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Basic information

Entry
Database: PDB / ID: 3o12
TitleThe crystal structure of a functionally unknown protein from Saccharomyces cerevisiae.
ComponentsUncharacterized protein YJL217W
Keywordsstructural genomics / unknown function / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


Protein of unknown function DUF1349 / Uncharacterised conserved protein UCP022704 / Protein of unknown function (DUF1349) / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Regulation of enolase protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsZhang, R. / Tan, K. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The crystal structure of a functionally unknown protein from Saccharomyces cerevisiae.
Authors: Zhang, R. / Tan, K. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJul 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YJL217W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4359
Polymers24,8031
Non-polymers6338
Water3,207178
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.665, 112.665, 92.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-339-

HOH

Detailsexperimentally unknown. It is predicted to be monomeric.

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Components

#1: Protein Uncharacterized protein YJL217W


Mass: 24802.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HRC198, J0226 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P40893
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate, 0.2M K/Na Tartrate, 2M Ammonium sulfate, 1/10 Elastase, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 27, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.5→34 Å / Num. all: 36147 / Num. obs: 36147 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 37.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1766 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→33.604 Å / SU ML: 0.15 / σ(F): 0.02 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1853 1751 4.98 %random
Rwork0.1668 ---
all0.1676 35161 --
obs0.1676 35161 96.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.178 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.2379 Å2-0 Å20 Å2
2---3.2379 Å2-0 Å2
3---6.4759 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1449 0 36 178 1663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061588
X-RAY DIFFRACTIONf_angle_d1.1352164
X-RAY DIFFRACTIONf_dihedral_angle_d13.565570
X-RAY DIFFRACTIONf_chiral_restr0.078233
X-RAY DIFFRACTIONf_plane_restr0.004272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.499-1.55250.23761510.20532992X-RAY DIFFRACTION87
1.5525-1.61470.19841710.17343148X-RAY DIFFRACTION93
1.6147-1.68820.21231700.16293254X-RAY DIFFRACTION95
1.6882-1.77720.18861720.16743342X-RAY DIFFRACTION97
1.7772-1.88850.17071750.16193369X-RAY DIFFRACTION98
1.8885-2.03430.17051980.15383402X-RAY DIFFRACTION100
2.0343-2.2390.1782000.15673411X-RAY DIFFRACTION100
2.239-2.56290.20471850.16983453X-RAY DIFFRACTION100
2.5629-3.22860.19851670.17713474X-RAY DIFFRACTION100
3.2286-33.61270.1561620.1533565X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 12.1017 Å / Origin y: 16.0684 Å / Origin z: 19.6659 Å
111213212223313233
T0.1212 Å2-0.0234 Å20.0043 Å2-0.0981 Å2-0.0221 Å2--0.0995 Å2
L1.3792 °20.0344 °20.0686 °2-0.4183 °2-0.3581 °2--0.8617 °2
S0.0101 Å °-0.049 Å °0.042 Å °0.0927 Å °-0.0201 Å °-0.0041 Å °-0.0882 Å °-0.0235 Å °0.0114 Å °
Refinement TLS groupSelection details: chain A

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