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Open data
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Basic information
Entry | Database: PDB / ID: 1w30 | ||||||
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Title | PyrR of Mycobacterium Tuberculosis as a potential drug target | ||||||
![]() | PYRR BIFUNCTIONAL PROTEIN | ||||||
![]() | TRANSFERASE / PYRR / GLYCOSYLTRANSFERASE / PSI / PROTEIN STRUCTURE INITIATIVE / TB STRUCTURAL GENOMICS CONSORTIUM / TB / TBSGC | ||||||
Function / homology | ![]() uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / nucleoside metabolic process / peptidoglycan-based cell wall / regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.2 KB | Display | ![]() |
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PDB format | ![]() | 66.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.3 KB | Display | ![]() |
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Full document | ![]() | 442.1 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 27.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1a3cS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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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: |
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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.) ![]() ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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