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- PDB-1jd1: Crystal Structure of YEO7_yeast -

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Basic information

Entry
Database: PDB / ID: 1jd1
TitleCrystal Structure of YEO7_yeast
ComponentsHYPOTHETICAL 13.9 KDA PROTEIN IN FCY2-PET117 INTERGENIC REGION
KeywordsTRANSLATION INHIBITOR / STRUCTURAL GENOMICS / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Threonine catabolism / organonitrogen compound catabolic process / deaminase activity / mitochondrial intermembrane space / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsDeaconescu, A.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proteins / Year: 2002
Title: X-ray structure of Saccharomyces cerevisiae homologous mitochondrial matrix factor 1 (Hmf1).
Authors: Deaconescu, A.M. / Roll-Mecak, A. / Bonanno, J.B. / Gerchman, S.E. / Kycia, H. / Studier, F.W. / Burley, S.K.
History
DepositionJun 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: HYPOTHETICAL 13.9 KDA PROTEIN IN FCY2-PET117 INTERGENIC REGION
B: HYPOTHETICAL 13.9 KDA PROTEIN IN FCY2-PET117 INTERGENIC REGION
C: HYPOTHETICAL 13.9 KDA PROTEIN IN FCY2-PET117 INTERGENIC REGION
D: HYPOTHETICAL 13.9 KDA PROTEIN IN FCY2-PET117 INTERGENIC REGION
E: HYPOTHETICAL 13.9 KDA PROTEIN IN FCY2-PET117 INTERGENIC REGION
F: HYPOTHETICAL 13.9 KDA PROTEIN IN FCY2-PET117 INTERGENIC REGION


Theoretical massNumber of molelcules
Total (without water)83,5136
Polymers83,5136
Non-polymers00
Water11,422634
1
A: HYPOTHETICAL 13.9 KDA PROTEIN IN FCY2-PET117 INTERGENIC REGION
B: HYPOTHETICAL 13.9 KDA PROTEIN IN FCY2-PET117 INTERGENIC REGION
F: HYPOTHETICAL 13.9 KDA PROTEIN IN FCY2-PET117 INTERGENIC REGION


Theoretical massNumber of molelcules
Total (without water)41,7573
Polymers41,7573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-42 kcal/mol
Surface area13060 Å2
MethodPISA
2
C: HYPOTHETICAL 13.9 KDA PROTEIN IN FCY2-PET117 INTERGENIC REGION
D: HYPOTHETICAL 13.9 KDA PROTEIN IN FCY2-PET117 INTERGENIC REGION
E: HYPOTHETICAL 13.9 KDA PROTEIN IN FCY2-PET117 INTERGENIC REGION


Theoretical massNumber of molelcules
Total (without water)41,7573
Polymers41,7573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-43 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.180, 64.100, 80.850
Angle α, β, γ (deg.)90.00, 90.63, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a trimer.

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Components

#1: Protein
HYPOTHETICAL 13.9 KDA PROTEIN IN FCY2-PET117 INTERGENIC REGION


Mass: 13918.897 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YERO57C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40037
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 634 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
2100 mM1dropNaCl
320 mMTris-Cl1drop
410 mMdithiothreitol1drop
51.9 Mammonium sulfate1reservoir
6100 mMsuccinate1reservoir

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98091, 0.99104
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 24, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.980911
20.991041
ReflectionResolution: 1.7→50 Å / Num. obs: 86368 / % possible obs: 99 % / Observed criterion σ(F): 0 / Redundancy: 4 % / Biso Wilson estimate: 20.16 Å2 / Rsym value: 0.035 / Net I/σ(I): 30
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 4 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.307 / % possible all: 97.7
Reflection
*PLUS
Num. obs: 88185 / % possible obs: 98.7 % / Num. measured all: 1452497 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 97.1 % / Rmerge(I) obs: 0.333

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.7→50 Å / Isotropic thermal model: anisotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.238 -Random
Rwork0.207 --
all-165416 -
obs-156294 -
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5483 0 0 634 6117
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 1.7→1.71 Å
RfactorNum. reflection% reflection
Rfree0.271 234 -
Rwork0.241 --
obs-2136 97.7 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 50 Å / σ(F): 2 / Rfactor obs: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.271 / Rfactor Rwork: 0.241

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