+Open data
-Basic information
Entry | Database: PDB / ID: 1jd1 | ||||||
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Title | Crystal Structure of YEO7_yeast | ||||||
Components | HYPOTHETICAL 13.9 KDA PROTEIN IN FCY2-PET117 INTERGENIC REGION | ||||||
Keywords | TRANSLATION INHIBITOR / STRUCTURAL GENOMICS / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information Threonine catabolism / : / deaminase activity / mitochondrial intermembrane space / mitochondrion / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Deaconescu, A.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jd1.cif.gz | 155.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jd1.ent.gz | 124.3 KB | Display | PDB format |
PDBx/mmJSON format | 1jd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jd1_validation.pdf.gz | 393.8 KB | Display | wwPDB validaton report |
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Full document | 1jd1_full_validation.pdf.gz | 405.7 KB | Display | |
Data in XML | 1jd1_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 1jd1_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/1jd1 ftp://data.pdbj.org/pub/pdb/validation_reports/jd/1jd1 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a trimer. |
-Components
#1: Protein | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.27 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 170 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98091, 0.99104 | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 24, 2000 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→50 Å / Isotropic thermal model: anisotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.71 Å
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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 |