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Yorodumi- PDB-4bjh: Crystal Structure of the Aquifex Reactor Complex Formed by Dihydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bjh | ||||||
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Title | Crystal Structure of the Aquifex Reactor Complex Formed by Dihydroorotase (H180A, H232A) with Dihydroorotate and Aspartate Transcarbamoylase with N-(phosphonacetyl)-L-aspartate (PALA) | ||||||
Components |
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Keywords | HYDROLASE/TRANSFERASE / HYDROLASE-TRANSFERASE COMPLEX / PYRIMIDINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information allantoinase activity / dihydroorotase / purine nucleobase catabolic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / dihydroorotase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process ...allantoinase activity / dihydroorotase / purine nucleobase catabolic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / dihydroorotase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | AQUIFEX AEOLICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Edwards, B.F.P. / Martin, P.D. / Grimley, E. / Vaishnav, A. / Fernando, R. / Brunzelle, J.S. / Cordes, M. / Evans, H.G. / Evans, D.R. | ||||||
Citation | Journal: Bmc Biochem. / Year: 2013 Title: The Mononuclear Metal Center of Type-I Dihydroorotase from Aquifex Aeolicus. Authors: Edwards, B.F. / Fernando, R. / Martin, P.D. / Grimley, E. / Cordes, M. / Vaishnav, A. / Brunzelle, J.S. / Evans, H.G. / Evans, D.R. #1: Journal: Biochemistry / Year: 2009 Title: Dihydroorotase from the Hyperthermophile Aquifex Aeolicus is Activated by Stoichiometric Association with Aspartate Transcarbamoylase and Forms a One-Pot Reactor for Pyrimidine Biosynthesis. Authors: Zhang, P. / Martin, P.D. / Purcarea, C. / Vaishnav, A. / Brunzelle, J.S. / Fernando, R. / Guy-Evans, H.I. / Evans, D.R. / Edwards, B.F.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bjh.cif.gz | 317 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bjh.ent.gz | 256.1 KB | Display | PDB format |
PDBx/mmJSON format | 4bjh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/4bjh ftp://data.pdbj.org/pub/pdb/validation_reports/bj/4bjh | HTTPS FTP |
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-Related structure data
Related structure data | 3d6nS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 50301.902 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) Description: GIFT FROM DRS KARL O. STETTER AND ROBERT HUBER, REGENSBURG UNIVERSITY, D-93053 REGENSBURG, GERMANY Plasmid: PAAPYRC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66990, dihydroorotase |
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#2: Protein | Mass: 37143.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) Description: GIFT FROM DRS KARL O. STETTER AND ROBERT HUBER, REGENSBURG UNIVERSITY, D-93053 REGENSBURG, GERMANY Plasmid: PAAPYRB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66726, aspartate carbamoyltransferase |
-Non-polymers , 7 types, 464 molecules
#3: Chemical | ChemComp-ZN / | ||||
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#4: Chemical | ChemComp-DOR / ( | ||||
#5: Chemical | ChemComp-PAL / | ||||
#6: Chemical | ChemComp-PO4 / | ||||
#7: Chemical | #8: Chemical | ChemComp-EDO / #9: 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: 3.17 Å3/Da / Density % sol: 61.2 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5 Details: THE CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN HANGING-DROPS. THE HETERO DODECAMER WAS BUFFER EXCHANGED INTO 10 MM HEPES, 1 MM TCEP PH 7.5, AT A FINAL PROTEIN CONCENTRATION OF 3.0 MG/ML. DHO- ...Details: THE CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN HANGING-DROPS. THE HETERO DODECAMER WAS BUFFER EXCHANGED INTO 10 MM HEPES, 1 MM TCEP PH 7.5, AT A FINAL PROTEIN CONCENTRATION OF 3.0 MG/ML. DHO-ATC SOLUTION (3-6 UL) WAS MIXED WITH 1 UL OF RESERVOIR SOLUTION (30% ETHYLENE GLYCOL) FOLLOWED BY 10% OF THE DROP VOLUME (V/V) OF 100 MM BARIUM CHLORIDE. THE FINAL CRYSTALLIZATION PH WAS 6.3. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 |
Detector | Type: MARRESEARCH MAR300 / Detector: CCD / Date: May 29, 2009 / Details: BE LENSES |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→77.85 Å / Num. obs: 53365 / % possible obs: 99.9 % / Redundancy: 8.8 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3D6N Resolution: 2.2→77.85 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.853 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL ATOMS IN RESIDUES MET1-ASP422 IN DHO AND RESIDUES MET1- -THR291 IN ATC ARE INCLUDED IN THE REFINEMENT AT FULL WEIGHT. ALL RESIDUES ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL ATOMS IN RESIDUES MET1-ASP422 IN DHO AND RESIDUES MET1- -THR291 IN ATC ARE INCLUDED IN THE REFINEMENT AT FULL WEIGHT. ALL RESIDUES EXCEPT MET1, LEU2, AND GLU42 IN DHO AND MET1 IN ATC HAVE ELECTRON DENSITY AT 1 SIGMA FOR ALL MAIN CHAIN ATOMS. RESIDUES LYS3, ILE5, LYS7, LYS33, LEU39, VAL40, GLU42, ALA43, LYS49, AND ALA373 IN THE COMPOSITE DOMAIN OF DHO, WHICH COMPRISES RESIDUES 1-55 PLUS 366-422, HAVE NO DENSITY AT 1 SIGMA FOR THEIR SIDE CHAINS, ALTHOUGH ALL OF THEM HAVE ELECTRON DENSITY FOR ONE OR MORE SIDE CHAIN ATOMS AT 0.5 SIGMA. SEVEN OF THESE RESIDUES OCCUR WITHIN THE LEAST DEFINED SEGMENT OF THE DHO SUBUNIT, ILE24-LYS49.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.256 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→77.85 Å
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