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- PDB-3b4t: Crystal structure of Mycobacterium tuberculosis RNase PH, the Myc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3b4t | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis RNase PH, the Mycobacterium tuberculosis Structural Genomics Consortium target Rv1340 | ||||||
![]() | Ribonuclease PH | ||||||
![]() | TRANSFERASE / RNase / tRNA nucleotidyltransferase / ribonuclease / RPHA / Structural Genomics / TBSGC / Mycobacterium tuberculosis Structural Genomics Consortium / tRNA processing / TB Structural Genomics Consortium / PSI / Protein Structure Initiative | ||||||
Function / homology | ![]() tRNA nucleotidyltransferase / tRNA nucleotidyltransferase activity / rRNA catabolic process / tRNA processing / rRNA processing / 3'-5'-RNA exonuclease activity / tRNA binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Antczak, A.J. / Berger, J.M. / Lekin, T. / Segelke, B.W. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB) / TB Structural Genomics Consortium (TBSGC) | ||||||
![]() | ![]() Title: 2.1 A Crystal structure of RNase PH from Mycobacterium tuberculosis. Authors: Antczak, A.J. / Lekin, T. / Segelke, B.W. / Berger, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 295.3 KB | Display | ![]() |
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PDB format | ![]() | 240.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 489.5 KB | Display | ![]() |
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Full document | ![]() | 511.5 KB | Display | |
Data in XML | ![]() | 64.6 KB | Display | |
Data in CIF | ![]() | 91.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1r6mS 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
#1: Protein | Mass: 27631.283 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q10628, UniProt: P9WGZ7*PLUS, tRNA nucleotidyltransferase #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.78 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 298 K / pH: 7.5 Details: 22.5% PEG 2000, 0.1M MOPS pH 7.5, 0.085M NaH2PO4, 0.085M K2HPO4, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 2, 2005 |
Radiation | Monochromator: DOUBLE FLAT CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→78.811 Å / Num. obs: 399198 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.054 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.09→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.58 / Rsym value: 0.54 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1R6M Resolution: 2.1→39.69 Å / Isotropic thermal model: ANISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED IN PHASING
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Displacement parameters | Biso mean: 39.67 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→39.69 Å
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LS refinement shell | Resolution: 2.1→2.12 Å
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