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- PDB-1xe7: Crystal structure of the YML079w protein from Saccharomyces cerev... -

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Basic information

Entry
Database: PDB / ID: 1xe7
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


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
ACETIC ACID / GUANINE / Uncharacterized protein YML079W
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)69,17113
Polymers68,2853
Non-polymers88610
Water4,468248
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)46,19610
Polymers45,5232
Non-polymers6738
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint8 kcal/mol
Surface area16960 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)45,9506
Polymers45,5232
Non-polymers4264
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)206.800, 206.800, 206.800
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: 22761.709 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-GUN / GUANINE / Guanine


Mass: 151.126 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H5N5O
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 283 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 283K

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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: 1.7→20 Å / Num. obs: 81006 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Biso Wilson estimate: 21.5 Å2 / Rsym value: 0.08 / Net I/σ(I): 14.3
Reflection shellResolution: 1.7→1.8 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.59 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: YML079wp

Resolution: 1.75→10 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 11366119.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3759 5.1 %RANDOM
Rwork0.22 ---
obs0.22 74257 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.1065 Å2 / ksol: 0.478675 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4520 0 57 252 4829
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 605 4.9 %
Rwork0.264 11689 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GUN.PARAMGUN.TOP

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