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Yorodumi- PDB-3ssz: The crystal structure of Mandelate racemase/muconate lactonizing ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ssz | ||||||
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Title | The crystal structure of Mandelate racemase/muconate lactonizing enzyme from Rhodobacteraceae bacterium | ||||||
Components | Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein | ||||||
Keywords | METAL BINDING PROTEIN / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / enolase | ||||||
Function / homology | Function and homology information L-lyxonate dehydratase / 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 ...L-lyxonate dehydratase / 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 | Rhodobacteraceae bacterium KLH11 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.392 Å | ||||||
Authors | Zhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Zhang, Z. / 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: The crystal structure of Mandelate racemase/muconate lactonizing enzyme from Rhodobacteraceae bacterium Authors: Zhang, Z. / 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 | 3ssz.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ssz.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ssz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ssz_validation.pdf.gz | 441 KB | Display | wwPDB validaton report |
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Full document | 3ssz_full_validation.pdf.gz | 444.1 KB | Display | |
Data in XML | 3ssz_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 3ssz_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ss/3ssz ftp://data.pdbj.org/pub/pdb/validation_reports/ss/3ssz | HTTPS FTP |
-Related structure data
Related structure data | 3fxgS 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Components
#1: Protein | Mass: 46598.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacteraceae bacterium KLH11 (bacteria) Gene: RKLH11_3829 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: B9NY46 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.92 Å3/Da / Density % sol: 57.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Bis-Tris pH 5.5, 2.0 Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2011 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→50 Å / Num. obs: 22070 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 25.1 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.39→2.48 Å / Redundancy: 20.3 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 17.5 / Num. unique all: 2163 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FXG Resolution: 2.392→48.358 Å / SU ML: 0.63 / Isotropic thermal model: Isotropic / σ(F): 1.4 / Phase error: 21.5 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.321 Å2 / ksol: 0.346 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.392→48.358 Å
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Refine LS restraints |
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LS refinement shell |
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