+Open data
-Basic information
Entry | Database: PDB / ID: 1ax4 | ||||||
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Title | TRYPTOPHANASE FROM PROTEUS VULGARIS | ||||||
Components | TRYPTOPHANASE | ||||||
Keywords | TRYPTOPHAN BIOSYNTHESIS / TRYPTOPHAN INDOLE-LYASE / PYRIDOXAL 5'-PHOSPHATE / MONOVALENT CATION BINDING SITE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Proteus vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Isupov, M.N. / Antson, A.A. / Dodson, E.J. / Dodson, G.G. / Dementieva, I.S. / Zakomirdina, L.N. / Wilson, K.S. / Dauter, Z. / Lebedev, A.A. / Harutyunyan, E.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Crystal structure of tryptophanase. Authors: Isupov, M.N. / Antson, A.A. / Dodson, E.J. / Dodson, G.G. / Dementieva, I.S. / Zakomirdina, L.N. / Wilson, K.S. / Dauter, Z. / Lebedev, A.A. / Harutyunyan, E.H. #1: Journal: Biochemistry of Vitamin B6 and Pqq / Year: 1994 Title: X-Ray Study of Tryptophanase at 2.1 Angstrom Resolution Authors: Isupov, M. / Dementieva, I. / Zakomirdina, L. / Wilson, K.S. / Dauter, Z. / Antson, A.A. / Dodson, G.G. / Harutyunyan, E.H. #2: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Preliminary X-Ray Investigation of Holotryptophanases from Escherichia Coli and Proteus Vulgaris Authors: Dementieva, I.S. / Zakomirdina, L.N. / Sinitzina, N.I. / Antson, A.A. / Wilson, K.S. / Isupov, M.N. / Lebedev, A.A. / Harutyunyan, E.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ax4.cif.gz | 386.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ax4.ent.gz | 318.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ax4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ax4_validation.pdf.gz | 459.3 KB | Display | wwPDB validaton report |
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Full document | 1ax4_full_validation.pdf.gz | 499.3 KB | Display | |
Data in XML | 1ax4_validation.xml.gz | 78.1 KB | Display | |
Data in CIF | 1ax4_validation.cif.gz | 109.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/1ax4 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/1ax4 | HTTPS FTP |
-Related structure data
Related structure data | 1tplS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 52787.102 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: PYRIDOXAL 5'-DEPENDENT ENZYME, REQUIRES MONOVALENT CATIONS FOR ACTIVITY, DEGRADES L-TRYPTOPHAN TO INDOLE, PYRUVATE AND AMMONIA Source: (gene. exp.) Proteus vulgaris (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P28796, tryptophanase #2: Chemical | ChemComp-K / #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: 2.49 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.8 Details: 27 % PEG 4000, 0.1 M POTASSIUM PHOSPHATE BUFFER PH 7.8, 0.25 MM PYRIDOXAL 5'-PHOSPHATE, 5MM DTT, 0.1 M CSCL. | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.95 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→18 Å / Num. obs: 397510 / % possible obs: 97.6 % / Redundancy: 3.33 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 2.49 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.273 / % possible all: 97.3 |
Reflection | *PLUS Num. obs: 117863 / Num. measured all: 397510 |
Reflection shell | *PLUS % possible obs: 97.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TYROSINE PHENOL LYASE, PDB ENTRY 1TPL Resolution: 2.1→18 Å / Cross valid method: FREE R
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Refinement step | Cycle: LAST / Resolution: 2.1→18 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 117863 / Rfactor obs: 0.187 | ||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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