+Open data
-Basic information
Entry | Database: PDB / ID: 1mb9 | ||||||
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Title | BETA-LACTAM SYNTHETASE COMPLEXED WITH ATP | ||||||
Components | BETA-LACTAM SYNTHETASE | ||||||
Keywords | HYDROLASE / CLAVULANIC ACID / ASPARAGINE SYNTHETASE / BETA-LACTAM SYNTHETASE / CARBOXYETHYL ARGININE / DEOXYGUANIDINOPROCLAVAMINIC ACID | ||||||
Function / homology | Function and homology information (carboxyethyl)arginine beta-lactam-synthase / (carboxyethyl)arginine beta-lactam-synthase activity / asparagine synthase (glutamine-hydrolyzing) activity / asparagine biosynthetic process / clavulanic acid biosynthetic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces clavuligerus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Miller, M.T. / Bachmann, B.O. / Townsend, C.A. / Rosenzweig, A.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: The catalytic cycle of beta -lactam synthetase observed by x-ray crystallographic snapshots Authors: Miller, M.T. / Bachmann, B.O. / Townsend, C.A. / Rosenzweig, A.C. | ||||||
History |
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Remark 600 | HETEROGEN ATP 701 HAS AN ALTERNATE CONFORMATION 'A'. AMP 706 AND POP 705 HAS ALTERNATE CONFORMATION 'B'. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mb9.cif.gz | 209.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mb9.ent.gz | 165.2 KB | Display | PDB format |
PDBx/mmJSON format | 1mb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/1mb9 ftp://data.pdbj.org/pub/pdb/validation_reports/mb/1mb9 | HTTPS FTP |
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-Related structure data
Related structure data | 1m1zC 1mbzC 1mc1C 1jgtS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 54601.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Gene: 1901 / Plasmid: pET24a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9R8E3, UniProt: P0DJQ7*PLUS |
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-Non-polymers , 5 types, 478 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-POP / | #4: Chemical | ChemComp-AMP / | #5: Chemical | #6: 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: 2.22 Å3/Da / Density % sol: 44.68 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 4000, Magnesium Chloride, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Miller, M.T., (2001) Nature Struct. Biol., 8, 684. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 21, 2000 |
Radiation | Monochromator: Curved Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→25 Å / Num. all: 64591 / Num. obs: 54280 / % possible obs: 99.6 % / Observed criterion σ(I): 5 / Biso Wilson estimate: 7.1 Å2 / Rsym value: 0.084 |
Reflection shell | Resolution: 2.11→2.19 Å / Rsym value: 0.296 / % possible all: 98.5 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 25 Å / Num. measured all: 594199 / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 98.5 % / Rmerge(I) obs: 0.296 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JGT Resolution: 2.11→24.78 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): -3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.97 Å2 / ksol: 0.378188 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.7 Å2
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Refine analyze | Luzzati coordinate error free: 0.3 Å / Luzzati sigma a free: 0.24 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→24.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.24 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 25 Å / % reflection Rfree: 7.8 % / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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