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- PDB-1ct5: CRYSTAL STRUCTURE OF YEAST HYPOTHETICAL PROTEIN YBL036C-SELENOMET... -

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Basic information

Entry
Database: PDB / ID: 1ct5
TitleCRYSTAL STRUCTURE OF YEAST HYPOTHETICAL PROTEIN YBL036C-SELENOMET CRYSTAL
ComponentsPROTEIN (YEAST HYPOTHETICAL PROTEIN, SELENOMET)
KeywordsSTRUCTURAL GENOMICS / TIM BARREL / YEAST / PYRIDOXAL-5'-PHOSPHATE / SELENOMETHIONINE / MAD / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


vitamin B6 metabolic process / pyridoxal phosphate binding / nucleus / cytoplasm
Similarity search - Function
Uncharacterized protein family UPF0001 signature. / Pyridoxal phosphate homeostasis protein / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Alanine racemase / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Pyridoxal phosphate homeostasis protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsEswaramoorthy, S. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of a yeast hypothetical protein selected by a structural genomics approach.
Authors: Eswaramoorthy, S. / Gerchman, S. / Graziano, V. / Kycia, H. / Studier, F.W. / Swaminathan, S.
History
DepositionAug 18, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 3, 2021Group: Derived calculations / Structure summary / Category: audit_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 26, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (YEAST HYPOTHETICAL PROTEIN, SELENOMET)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4212
Polymers29,1741
Non-polymers2471
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.052, 65.823, 93.052
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (YEAST HYPOTHETICAL PROTEIN, SELENOMET)


Mass: 29173.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YBL 036C / Plasmid: PET-13A B834(DE3) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38197
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.58 Å3/Da / Density % sol: 0.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG 4000, 0.1M sodium citrate, 0.2M ammonium acetate, 2.9 mg/ml protein in 6.25mM HEPES and 62.5mM NaCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal
*PLUS
Crystal grow
*PLUS
pH: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.2 Mammonium sulfate1reservoir
30.2 Msodium acetate1reservoir
430 %mPEG20001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9803
DetectorType: BRANDEIS / Detector: CCD / Date: Nov 12, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9803 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 20510 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 7.7
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.253 / % possible all: 94.9
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Num. measured all: 138645 / Biso Wilson estimate: 19 Å2
Reflection shell
*PLUS
% possible obs: 94.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
SHARPphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 2→12.5 Å / Cross valid method: FREE R / ESU R: 0.17 / ESU R Free: 0.16
RfactorNum. reflectionSelection details
Rfree0.245 1060 RANDOM
Rwork0.196 --
obs-19399 -
Refinement stepCycle: LAST / Resolution: 2→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 15 204 2031
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0350.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 12.5 Å / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS

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