+Open data
-Basic information
Entry | Database: PDB / ID: 1w30 | ||||||
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Title | PyrR of Mycobacterium Tuberculosis as a potential drug target | ||||||
Components | PYRR BIFUNCTIONAL PROTEIN | ||||||
Keywords | TRANSFERASE / PYRR / GLYCOSYLTRANSFERASE / PSI / PROTEIN STRUCTURE INITIATIVE / TB STRUCTURAL GENOMICS CONSORTIUM / TB / TBSGC | ||||||
Function / homology | Function and homology information uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / nucleoside metabolic process / peptidoglycan-based cell wall / regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kantardjieff, K.A. / Vasquez, C. / Castro, P. / Warfel, N.N. / Rho, B.-S. / Lekin, T. / Kim, C.-Y. / Segelke, B.W. / Terwilliger, T. / Rupp, B. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of Pyrr (Rv1379) from Mycobacterium Tuberculosis: A Persistence Gene and Protein Drug Target Authors: Kantardjieff, K.A. / Vasquez, C. / Castro, P. / Warfel, N.N. / Rho, B.-S. / Lekin, T. / Kim, C.-Y. / Segelke, B.W. / Terwilliger, T. / Rupp, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w30.cif.gz | 87.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w30.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 1w30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w30_validation.pdf.gz | 433.3 KB | Display | wwPDB validaton report |
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Full document | 1w30_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 1w30_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 1w30_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/1w30 ftp://data.pdbj.org/pub/pdb/validation_reports/w3/1w30 | HTTPS FTP |
-Related structure data
Related structure data | 1a3cS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 4
NCS oper: (Code: given Matrix: (-0.3662, -0.3354, 0.868), Vector: |
-Components
#1: Protein | Mass: 21629.594 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: GSHHHHHH C-TERMINAL TAG / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: HRV37 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P71807, UniProt: P9WHK3*PLUS, uracil phosphoribosyltransferase #2: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | D21N MUTATION, C-TERMINAL GSHHHHHH TAG | |
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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: 2.3 Å3/Da / Density % sol: 46.5 % Description: 3D-PSSM HOMOLOGY MODEL FROM 1A3C REFINED WITH SCWRL 3.0 |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: SITTING DROPS 0.5UL + 0.5UL IN INTELLIPLATE, 0.1M IMIDAZOLE-MALEATE PH 7.5, 26% PEG-MME 2K, 2.8% EDTA. CRYSTAL APPROXIMATELY 50 MICRON RHOMBOID. |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 15, 2003 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→38.8 Å / Num. obs: 34571 / % possible obs: 99.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 4 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A3C Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.611 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N-TERMINAL REGION 1-11 ABSENT IN DENSITY. LOOPS 90-100 HIGHLY FLEXIBLE AND ABSENT FROM MODEL, ALTHOUGH INTERMITTENT DENSITY FRAGMENTS CAN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N-TERMINAL REGION 1-11 ABSENT IN DENSITY. LOOPS 90-100 HIGHLY FLEXIBLE AND ABSENT FROM MODEL, ALTHOUGH INTERMITTENT DENSITY FRAGMENTS CAN BE TRACED. RESIDUE ATOMS. C -TERMINAL LINKER AND HIS TAG GSHHHHHH ABSENT FROM DENSITY, FRAGMENTS OF ISOLATED OR FRAGMENTED DENSITY ARE VISIBLE AND MAY BE REPRESENTED BY SOLVENT ATOMS. ALL REGIONS EXCLUDED FROM NCS SHOW HIGH MOBILITY AND VARIATION BETWEEN MOLECULES.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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