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Yorodumi- PDB-4a1o: Crystal structure of Mycobacterium tuberculosis PurH complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a1o | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis PurH complexed with AICAR and a novel nucleotide CFAIR, at 2.48 A resolution. | ||||||
Components | BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH | ||||||
Keywords | TRANSFERASE-HYDROLASE | ||||||
Function / homology | Function and homology information phosphoribosylaminoimidazolecarboxamide formyltransferase / phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase / IMP cyclohydrolase activity / 'de novo' IMP biosynthetic process / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å | ||||||
Authors | Le Nours, J. / Bulloch, E.M.M. / Zhang, Z. / Greenwood, D.R. / Middleditch, M.J. / Dickson, J.M.J. / Baker, E.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural Analyses of a Purine Biosynthetic Enzyme from Mycobacterium Tuberculosis Reveal a Novel Bound Nucleotide. Authors: Le Nours, J. / Bulloch, E.M.M. / Zhang, Z. / Greenwood, D.R. / Middleditch, M.J. / Dickson, J.M.J. / Baker, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a1o.cif.gz | 396 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a1o.ent.gz | 324.6 KB | Display | PDB format |
PDBx/mmJSON format | 4a1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a1o_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4a1o_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4a1o_validation.xml.gz | 39.7 KB | Display | |
Data in CIF | 4a1o_validation.cif.gz | 55.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/4a1o ftp://data.pdbj.org/pub/pdb/validation_reports/a1/4a1o | HTTPS FTP |
-Related structure data
Related structure data | 3zzmSC 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: (-0.9684, -0.2122, 0.1307), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 55084.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P67541, UniProt: P9WHM7*PLUS, phosphoribosylaminoimidazolecarboxamide formyltransferase, IMP cyclohydrolase |
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-Non-polymers , 5 types, 279 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-JLN / | #6: Water | ChemComp-HOH / | |
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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: NONE |
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Crystal grow | pH: 6.5 Details: 24-34% PEG 8000, 0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 29, 2007 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→50 Å / Num. obs: 38276 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 10.5 % / Biso Wilson estimate: 59.45 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.2→2.58 Å / Redundancy: 7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.7 / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZZM Resolution: 2.48→43.84 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.9241 / Cross valid method: THROUGHOUT / σ(F): 0 Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=K AMZ JLN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE= 7962. NUMBER WITH APPROX ...Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=K AMZ JLN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE= 7962. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=68. NUMBER RESTRAINT LSSR (-AUTONCS).
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Displacement parameters | Biso mean: 51.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2.48→43.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.48→2.55 Å / Total num. of bins used: 19
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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