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- PDB-1b54: CRYSTAL STRUCTURE OF A YEAST HYPOTHETICAL PROTEIN-A STRUCTURE FRO... -

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Basic information

Entry
Database: PDB / ID: 1b54
TitleCRYSTAL STRUCTURE OF A YEAST HYPOTHETICAL PROTEIN-A STRUCTURE FROM BNL'S HUMAN PROTEOME PROJECT
ComponentsYEAST HYPOTHETICAL PROTEIN
KeywordsHYPOTHETICAL PROTEIN / YEAST HYPOTHETICAL PROTEIN / PROTEOME / PYRIDOXAL PHOSPHATE / TIM BARREL / Structural Genomics / 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 / MIR / Resolution: 2.1 Å
AuthorsSwaminathan, S. / Eswaramoorthy, 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
DepositionJan 12, 1999Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
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: YEAST HYPOTHETICAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4112
Polymers29,1641
Non-polymers2471
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.580, 65.710, 91.940
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 YEAST HYPOTHETICAL PROTEIN


Mass: 29164.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C
Description: CHR II GENE OBTAINED BY PCR FROM S288C GENOMIC DNA CLONED INTO T7 EXPRESSION VECTOR PET13A AT NDEI-BAMHI SITES, NO CHANGES MADE TO GENOMIC SEQUENCE
Gene: SGD: YBL 036C / Plasmid: P07PLK / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / Strain (production host): PET / 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.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 52 %
Description: DERIVATIVE DATA SETS WERE COLLECTED AT X12C AND X12B OF NSLS, BNL.
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
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: X8C / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 17243 / % possible obs: 99.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.3
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.2 / % possible all: 96
Reflection
*PLUS
Num. measured all: 72799
Reflection shell
*PLUS
% possible obs: 96.4 % / Rmerge(I) obs: 0.206

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1642 10 %RANDOM
Rwork0.235 ---
obs0.235 16442 93.5 %-
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 15 162 2015
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.73
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.19 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.329 142 6.6 %
Rwork0.307 1349 -
obs--69 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.PLPTOPH19.SOL
X-RAY DIFFRACTION3TOP.PLP
X-RAY DIFFRACTION4TOP.LYSH
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.222 / Rfactor Rfree: 0.277
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.73
LS refinement shell
*PLUS
Rfactor obs: 0.307

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