+Open data
-Basic information
Entry | Database: PDB / ID: 3xim | ||||||
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Title | ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS | ||||||
Components | D-XYLOSE ISOMERASE | ||||||
Keywords | ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE) | ||||||
Function / homology | Function and homology information xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Actinoplanes missouriensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Mrabet, N.T. / Van Denbroek, A. / Van Den Brande, I. / Stanssens, P. / Laroche, Y. / Lambeir, A.-M. / Matthyssens, G. / Jenkins, J. / Chiadmi, M. / Vantilbeurgh, H. ...Mrabet, N.T. / Van Denbroek, A. / Van Den Brande, I. / Stanssens, P. / Laroche, Y. / Lambeir, A.-M. / Matthyssens, G. / Jenkins, J. / Chiadmi, M. / Vantilbeurgh, H. / Rey, F. / Janin, J. / Quax, W.J. / Lasters, I. / Demaeyer, M. / Wodak, S.J. | ||||||
Citation | Journal: Biochemistry / Year: 1992 Title: Arginine residues as stabilizing elements in proteins. Authors: Mrabet, N.T. / Van den Broeck, A. / Van den brande, I. / Stanssens, P. / Laroche, Y. / Lambeir, A.M. / Matthijssens, G. / Jenkins, J. / Chiadmi, M. / van Tilbeurgh, H. / Rey, F. / Janin, J. ...Authors: Mrabet, N.T. / Van den Broeck, A. / Van den brande, I. / Stanssens, P. / Laroche, Y. / Lambeir, A.M. / Matthijssens, G. / Jenkins, J. / Chiadmi, M. / van Tilbeurgh, H. / Rey, F. / Janin, J. / Quax, W.J. / Lasters, I. / Demaeyer, M. / Wodak, S.J. #1: Journal: Proteins / Year: 1988 Title: Structural Analysis of the 2.8 Angstroms Model of Xylose Isomerase from Actinoplanes Missouriensis Authors: Rey, F. / Jenkins, J. / Janin, J. / Lasters, I. / Alard, P. / Claessens, M. / Matthyssens, G. / Wodak, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3xim.cif.gz | 328.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3xim.ent.gz | 266.3 KB | Display | PDB format |
PDBx/mmJSON format | 3xim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3xim_validation.pdf.gz | 414.6 KB | Display | wwPDB validaton report |
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Full document | 3xim_full_validation.pdf.gz | 450.7 KB | Display | |
Data in XML | 3xim_validation.xml.gz | 34.9 KB | Display | |
Data in CIF | 3xim_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/3xim ftp://data.pdbj.org/pub/pdb/validation_reports/xi/3xim | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES PRO A 187, PRO B 187, PRO C 187, AND PRO D 187 ARE CIS PROLINES. | ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 43505.559 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinoplanes missouriensis (bacteria) / References: UniProt: P12851, xylose isomerase #2: Sugar | ChemComp-SOR / #3: Chemical | ChemComp-CO / #4: Water | ChemComp-HOH / | Compound details | THE THREE LYS TO ARG SUBSTITUTIONS AT SITES 309, 319, AND 323 YIELD A THERMOSTABLE ENZYME WITH WILD ...THE THREE LYS TO ARG SUBSTITUTI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.95 Å3/Da / Density % sol: 68.86 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.1 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.3 Å / Num. obs: 95937 / Num. measured all: 254909 / Rmerge(I) obs: 0.059 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Highest resolution: 2.3 Å Details: VAL 3 HAS WEAK DENSITY IN CHAINS A AND C, GLN 4 IN CHAIN 6.
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Refinement step | Cycle: LAST / Highest resolution: 2.3 Å
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Refine LS restraints |
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Refinement | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 18.8 Å2 |