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- PDB-1xe8: Crystal structure of the YML079w protein from Saccharomyces cerev... -

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Basic information

Entry
Database: PDB / ID: 1xe8
TitleCrystal structure of the YML079w protein from Saccharomyces cerevisiae reveals a new sequence family of the jelly roll fold.
ComponentsHypothetical 22.5 kDa protein in TUB1-CPR3 intergenic region
KeywordsStructural genomics / unknown function / jelly roll motif / cupin superfamily / YML079wp / S. cerevisiae
Function / homology
Function and homology information


pyrimidine-containing compound metabolic process / nucleus / cytoplasm
Similarity search - Function
Cupin domain of unknown function DUF985 / Uncharacterized protein YML079W-like / Cupin superfamily (DUF985) / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ADENINE / CITRIC ACID / Uncharacterized protein YML079W
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsZhou, C.-Z. / Meyer, P. / Quevillon-Cheruel, S. / Li de La Sierra-Gallay, I. / Collinet, B. / Graille, M. / Leulliot, N. / Sorel, I. / Janin, J. / Van Tilbeurgh, H.
CitationJournal: Protein Sci. / Year: 2005
Title: Crystal structure of the YML079w protein from Saccharomyces cerevisiae reveals a new sequence family of the jelly-roll fold
Authors: Zhou, C.-Z. / Meyer, P. / Quevillon-Cheruel, S. / Li de La Sierra-Gallay, I. / Collinet, B. / Graille, M. / Blondeau, K. / Leulliot, N. / Sorel, I. / Poupon, A. / Janin, J. / Van Tilbeurgh, H.
History
DepositionSep 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 13, 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_ref_seq_dif / 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_ref_seq_dif.details / _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: Hypothetical 22.5 kDa protein in TUB1-CPR3 intergenic region
B: Hypothetical 22.5 kDa protein in TUB1-CPR3 intergenic region
C: Hypothetical 22.5 kDa protein in TUB1-CPR3 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1276
Polymers68,7073
Non-polymers4193
Water3,243180
1
A: Hypothetical 22.5 kDa protein in TUB1-CPR3 intergenic region
B: Hypothetical 22.5 kDa protein in TUB1-CPR3 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1324
Polymers45,8052
Non-polymers3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-4 kcal/mol
Surface area17250 Å2
MethodPISA
2
C: Hypothetical 22.5 kDa protein in TUB1-CPR3 intergenic region
hetero molecules

C: Hypothetical 22.5 kDa protein in TUB1-CPR3 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9894
Polymers45,8052
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation42_654-x+3/2,z+1/2,y-1/21
Unit cell
Length a, b, c (Å)207.970, 207.970, 207.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein Hypothetical 22.5 kDa protein in TUB1-CPR3 intergenic region / YML079wp


Mass: 22902.395 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YML079w / Plasmid: PCRT7-CT-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLys / References: UniProt: Q03629
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.7 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20-24% PEG 4000, 0.1M Na-Citrate, 0.2M Ammonium Acetate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.93 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 1, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 19176 / Num. obs: 19176 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.8 % / Rsym value: 0.2 / Net I/σ(I): 22
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 6 / Rsym value: 0.62 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
SCALAdata scaling
SOLVEphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2844 922 -RANDOM
Rwork0.223 ---
all-19142 --
obs-18909 98.8 %-
Displacement parametersBiso mean: 26.4963 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4562 0 29 180 4771
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007712
X-RAY DIFFRACTIONc_angle_deg1.46164

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