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Yorodumi- PDB-3n4a: Crystal structure of D-Xylose Isomerase in complex with S-1,2-Pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n4a | ||||||
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Title | Crystal structure of D-Xylose Isomerase in complex with S-1,2-Propandiol | ||||||
Components | Xylose isomerase | ||||||
Keywords | ISOMERASE / INTRAMOLECULAR OXIDOREDUCTSE / S-1 / 2-Propandiol / TIM BARREL-BETA-ALPHA-BARRELS / TWO METAL BINDING ITES / Manganese | ||||||
Function / homology | Function and homology information xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces rubiginosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.94 Å | ||||||
Authors | Behnen, J. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Chemmedchem / Year: 2012 Title: Experimental and computational active site mapping as a starting point to fragment-based lead discovery. Authors: Behnen, J. / Koster, H. / Neudert, G. / Craan, T. / Heine, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n4a.cif.gz | 98.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n4a.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 3n4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n4a_validation.pdf.gz | 439 KB | Display | wwPDB validaton report |
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Full document | 3n4a_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | 3n4a_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 3n4a_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/3n4a ftp://data.pdbj.org/pub/pdb/validation_reports/n4/3n4a | HTTPS FTP |
-Related structure data
Related structure data | 3ms3C 3msaC 3msfC 3msnC 3n21C 3n9wC 3nn7C 3nx8C 3pczC 3prsC 3pvkC 3pwwC 1xicS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 43152.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-PGO / | #5: 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: 2.75 Å3/Da / Density % sol: 55.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 20-28% Propandiol, 0.2M MgCl, 50mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 11, 2009 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→25 Å / Num. obs: 34311 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rsym value: 0.049 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 1.94→1.97 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 1509 / Rsym value: 0.4 / % possible all: 88.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1XIC Resolution: 1.94→10 Å / Num. parameters: 13514 / Num. restraintsaints: 12544 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 2889 / Occupancy sum non hydrogen: 3355.22 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.97 Å / Num. reflection obs: 34311 |