+Open data
-Basic information
Entry | Database: PDB / ID: 1ydm | ||||||
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Title | X-Ray structure of Northeast Structural Genomics target SR44 | ||||||
Components | Hypothetical protein yqgN | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Northeast Structural Genomics / SR44 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information 5-formyltetrahydrofolate cyclo-ligase activity / folic acid-containing compound biosynthetic process / tetrahydrofolate interconversion / ATP binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Kuzin, A.P. / Jianwei, S. / Vorobiev, S. / Acton, T. / Xia, R. / Ma, L.-C. / Montelione, G. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: X-Ray structure of Northeast Structural Genomics target SR44 Authors: Kuzin, A.P. / Jianwei, S. / Vorobiev, S. / Acton, T. / Xia, R. / Ma, L.-C. / Montelione, G. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ydm.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ydm.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 1ydm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ydm_validation.pdf.gz | 454.4 KB | Display | wwPDB validaton report |
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Full document | 1ydm_full_validation.pdf.gz | 474.8 KB | Display | |
Data in XML | 1ydm_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 1ydm_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/1ydm ftp://data.pdbj.org/pub/pdb/validation_reports/yd/1ydm | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21580.375 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yqgN / Production host: Escherichia coli (E. coli) / References: UniProt: P54491 #2: Chemical | #3: 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: 2.3 Å3/Da / Density % sol: 46.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 26% PEG8000, 50 mM Tris, 0.2M AmSO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97859,0.97897,0.97243 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2003 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→30 Å / Num. all: 33714 / Num. obs: 18301 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Biso Wilson estimate: 40.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.5 | ||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.1 / % possible all: 75.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→28.35 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 485972.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.5 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 20.4111 Å2 / ksol: 0.292953 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→28.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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