+Open data
-Basic information
Entry | Database: PDB / ID: 1gvg | ||||||
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Title | Crystal Structure of Clavaminate Synthase with Nitric Oxide | ||||||
Components | CLAVAMINATE SYNTHASE 1 | ||||||
Keywords | OXIDOREDUCTASE / LYASE / OXYGENASE / TRIFUNCTIONAL ENZYME / CLAVAMINATE SYNTHASE 1 / JELLY ROLL / NITRIC OXIDE | ||||||
Function / homology | Function and homology information clavaminate synthase / clavaminate synthase activity / clavulanic acid biosynthetic process / antibiotic biosynthetic process / iron ion binding Similarity search - Function | ||||||
Biological species | STREPTOMYCES CLAVULIGERUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Zhang, Z.H. / Ren, J. / McKinnon, C.H. / Clifton, I.J. / Harlos, K. / Schofield, C.J. | ||||||
Citation | Journal: FEBS Lett. / Year: 2002 Title: Crystal Structure of a Clavaminate Synthase-Fe(II) -2-Oxoglutarate-Substrate-No Complex: Evidence for Metal Centered Rearrangements Authors: Zhang, Z.H. / Ren, J. / Harlos, K. / McKinnon, C.H. / Clifton, I.J. / Schofield, C.J. #1: Journal: Nat.Struct.Biol. / Year: 2000 Title: Structural Origins of the Selectivity of the Trifunctional Oxygenase Clavaminic Acid Synthase Authors: Zhang, Z.H. / Ren, J. / Stammers, D.K. / Baldwin, J.E. / Harlos, K. / Schofield, C.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gvg.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gvg.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 1gvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/1gvg ftp://data.pdbj.org/pub/pdb/validation_reports/gv/1gvg | HTTPS FTP |
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-Related structure data
Related structure data | 1ds0S 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35415.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q05581, clavaminate synthase |
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-Non-polymers , 6 types, 399 molecules
#2: Chemical | ChemComp-FE / | ||||||
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#3: Chemical | ChemComp-AKG / | ||||||
#4: Chemical | #5: Chemical | ChemComp-PCX / | #6: Chemical | ChemComp-HOA / | #7: 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: 2.2 Å3/Da / Density % sol: 43.65 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.6 / Details: pH 7.60 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200H / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→30 Å / Num. obs: 46381 / % possible obs: 97.7 % / Redundancy: 13.2 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.54→1.6 Å / Redundancy: 4.46 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3.8 / % possible all: 86 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 301822 |
Reflection shell | *PLUS % possible obs: 86 % / Num. unique obs: 4038 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DS0 Resolution: 1.54→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 46.29 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.54→30 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.2074 / Rfactor Rwork: 0.1813 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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