+Open data
-Basic information
Entry | Database: PDB / ID: 3c8t | ||||||
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Title | Crystal structure of fumarate lyase from Mesorhizobium sp. BNC1 | ||||||
Components | Fumarate lyase | ||||||
Keywords | LYASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information 3-carboxy-cis,cis-muconate cycloisomerase activity => GO:0047472 / 3-carboxy-cis,cis-muconate cycloisomerase / 3-carboxy-cis,cis-muconate cycloisomerase activity Similarity search - Function | ||||||
Biological species | Mesorhizobium sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Bonanno, J.B. / Freeman, J. / Bain, K.T. / Chang, S. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of fumarate lyase from Mesorhizobium sp. BNC1. Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Chang, S. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c8t.cif.gz | 96.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c8t.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 3c8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/3c8t ftp://data.pdbj.org/pub/pdb/validation_reports/c8/3c8t | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | AUTHORS STATE THAT THE TETRAMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION. |
-Components
#1: Protein | Mass: 49371.312 Da / Num. of mol.: 1 / Fragment: Residues 17-456 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mesorhizobium sp. (bacteria) / Strain: BNC1 / Gene: Meso_3622 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q11C84 |
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#2: 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: 2.16 Å3/Da / Density % sol: 43.06 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7.5 Details: 100mM Hepes pH 7.5, 5% MPD, 10% PEG 6000, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 9, 2007 |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→37.832 Å / Num. all: 22568 / Num. obs: 22568 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.18 / Rsym value: 0.18 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 8 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3225 / Rsym value: 0.506 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.204 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.296 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.067 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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