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Yorodumi- PDB-1qyi: X-RAY STRUCTURE OF Q8NW41 NORTHEAST STRUCTURAL GENOMICS CONSORTIU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qyi | ||||||
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Title | X-RAY STRUCTURE OF Q8NW41 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ZR25. | ||||||
Components | hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein / Uncharacterized protein Function and homology information | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Kuzin, A.P. / Edstrom, W. / Ma, L.C. / Shin, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: X-RAY STRUCTURE OF Q8NW41 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ZR25. Authors: Kuzin, A.P. / Edstrom, W. / Ma, L.C. / Shih, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qyi.cif.gz | 87 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qyi.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/1qyi ftp://data.pdbj.org/pub/pdb/validation_reports/qy/1qyi | HTTPS FTP |
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-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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Unit cell |
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-Components
#1: Protein | Mass: 44007.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Species: Staphylococcus aureus / Strain: MW2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NW41, UniProt: A0A0H3JXW6*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 0.2M Lithium nitrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97942, 0.97922, 0.97236 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2003 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→20 Å / Num. all: 27084 / Num. obs: 23940 / % possible obs: 89.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 | ||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.146 / % possible all: 71.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→19.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2866653.65 / Data cutoff high rms absF: 2866653.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 11.2875 Å2 / ksol: 0.256747 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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