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Yorodumi- PDB-6l2z: IlvC, a ketol-acid reductoisomerase, from Streptococcus pnuemonia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l2z | |||||||||||||||
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Title | IlvC, a ketol-acid reductoisomerase, from Streptococcus pnuemoniae_D191G | |||||||||||||||
Components | Ketol-acid reductoisomerase (NADP(+)) | |||||||||||||||
Keywords | ISOMERASE / IlvC / Stereptococcus pneumoniae / BCAA pathway / ketol-acid reductoisomerase / D191G | |||||||||||||||
Function / homology | Function and homology information ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / L-valine biosynthetic process / isoleucine biosynthetic process / NADP binding / magnesium ion binding Similarity search - Function | |||||||||||||||
Biological species | Streptococcus pneumoniae D39 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | |||||||||||||||
Authors | Gyuhee, K. / Donghyuk, S. / Sumin, L. / Jaesook, Y. / Sangho, L. | |||||||||||||||
Funding support | Korea, Republic Of, 4items
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Citation | Journal: Crystals / Year: 2019 Title: Crystal Structure of IlvC, a Ketol-Acid Reductoisomerase, from Streptococcus Pneumoniae. Authors: Kim, G.H. / Shin, D.H. / Lee, S.M. / Yoon, J.S. / Lee, S.H. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l2z.cif.gz | 188.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l2z.ent.gz | 119.1 KB | Display | PDB format |
PDBx/mmJSON format | 6l2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l2z_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 6l2z_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 6l2z_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 6l2z_validation.cif.gz | 47.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/6l2z ftp://data.pdbj.org/pub/pdb/validation_reports/l2/6l2z | HTTPS FTP |
-Related structure data
Related structure data | 6l2iSC 6l2kC 6l2rC 6l2sC 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37334.195 Da / Num. of mol.: 2 / Mutation: D191G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae D39 (bacteria) Strain: D39 / NCTC 7466 / Gene: ilvC, SPD_0406 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q04M32, ketol-acid reductoisomerase (NADP+) |
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-Non-polymers , 5 types, 559 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NH4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.71 Å3/Da / Density % sol: 54.63 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 0.1M HEPES pH 7.5, 0.1 M NaCl, 1.5 M ammonium sulfate, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→23.87 Å / Num. obs: 52903 / % possible obs: 98.1 % / Redundancy: 13.2 % / Biso Wilson estimate: 28.86 Å2 / CC1/2: 0.996 / Net I/σ(I): 54.6 |
Reflection shell | Resolution: 2.02→2.09 Å / Num. unique obs: 2650 / CC1/2: 0.993 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6L2I Resolution: 2.02→23.87 Å / SU ML: 0.2029 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.7558
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→23.87 Å
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Refine LS restraints |
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LS refinement shell |
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