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Yorodumi- PDB-2jcy: X-ray structure of mutant 1-deoxy-D-xylulose 5-phosphate reductoi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jcy | ||||||
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Title | X-ray structure of mutant 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis | ||||||
Components | 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE | ||||||
Keywords | OXIDOREDUCTASE / DOXP/MEP PATHWAY / ISOPRENE BIOSYNTHESIS / 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE / NADP / RV2870C / METAL-BINDING | ||||||
Function / homology | Function and homology information terpenoid biosynthetic process, mevalonate-independent / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process / 1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / cobalt ion binding / NADPH binding / manganese ion binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Henriksson, L.M. / Unge, T. / Jones, T.A. / Mowbray, S.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structures of Mycobacterium Tuberculosis 1-Deoxy-D- Xylulose-5-Phosphate Reductoisomerase Provide New Insights Into Catalysis. Authors: Henriksson, L.M. / Unge, T. / Carlsson, J. / Aqvist, J. / Mowbray, S.L. / Jones, T.A. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jcy.cif.gz | 154.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jcy.ent.gz | 121.7 KB | Display | PDB format |
PDBx/mmJSON format | 2jcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jcy_validation.pdf.gz | 434.3 KB | Display | wwPDB validaton report |
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Full document | 2jcy_full_validation.pdf.gz | 439 KB | Display | |
Data in XML | 2jcy_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 2jcy_validation.cif.gz | 43.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/2jcy ftp://data.pdbj.org/pub/pdb/validation_reports/jc/2jcy | HTTPS FTP |
-Related structure data
Related structure data | 2jcvC 2jcxC 2jd0C 2jd1C 2jd2C 4aicC 2c82S 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.4985, 0.8546, 0.1455), Vector: |
-Components
#1: Protein | Mass: 41699.000 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-389 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET101D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P64012, UniProt: P9WNS1*PLUS, 1-deoxy-D-xylulose-5-phosphate reductoisomerase #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASP 151 TO ASN ENGINEERED RESIDUE IN CHAIN A, GLU 222 TO GLN ...ENGINEERED | |
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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: 2.2 Å3/Da / Density % sol: 44.5 % |
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.042 |
Detector | Date: Apr 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.042 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→40 Å / Num. obs: 30603 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.35→2.41 Å / Rmerge(I) obs: 0.19 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C82 Resolution: 2.35→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.941 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.456 / ESU R Free: 0.256 / 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: 18.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→40 Å
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