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Yorodumi- PDB-3t9p: Crystal structure of a putative mandelate racemase/muconate lacto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t9p | ||||||
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Title | Crystal structure of a putative mandelate racemase/muconate lactonizing enzyme family protein from Roseovarius | ||||||
Components | Mandelate racemase/muconate lactonizing enzyme family protein | ||||||
Keywords | ISOMERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC | ||||||
Function / homology | Function and homology information Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal ...Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Roseovarius sp. TM1035 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Agarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Agarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a putative mandelate racemase/muconate lactonizing enzyme family protein from Roseovarius Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t9p.cif.gz | 165.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t9p.ent.gz | 130.4 KB | Display | PDB format |
PDBx/mmJSON format | 3t9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t9p_validation.pdf.gz | 473.6 KB | Display | wwPDB validaton report |
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Full document | 3t9p_full_validation.pdf.gz | 482.4 KB | Display | |
Data in XML | 3t9p_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 3t9p_validation.cif.gz | 51.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/3t9p ftp://data.pdbj.org/pub/pdb/validation_reports/t9/3t9p | HTTPS FTP |
-Related structure data
Related structure data | 3t8qS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43117.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Roseovarius sp. TM1035 (bacteria) / Strain: TM1035 / Gene: RTM1035_01290 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: A6E1Q0 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 2.91 Å3/Da / Density % sol: 57.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M NaCL, 0.1M HEPES pH 7.5, 1.6M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2011 / Details: mirrors |
Radiation | Monochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. all: 71641 / Num. obs: 71641 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 5 / Num. unique all: 7073 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3T8Q Resolution: 1.97→46.99 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.909 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.14 / ESU R Free: 0.135 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→46.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.971→2.022 Å / Total num. of bins used: 20
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