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Yorodumi- PDB-1qo2: Crystal structure of N-((5'-phosphoribosyl)-formimino)-5-aminoimi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qo2 | ||||||
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Title | Crystal structure of N-((5'-phosphoribosyl)-formimino)-5-aminoimidazol-4-carboxamid ribonucleotid isomerase (EC 3.1.3.15, HisA) | ||||||
Components | |||||||
Keywords | ISOMERASE / HISTIDINE BIOSYNTHESIS / THERMOPHILIC PROTEIN | ||||||
Function / homology | Function and homology information 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity / L-histidine biosynthetic process / tryptophan biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | THERMOTOGA MARITIMA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å | ||||||
Authors | Wilmanns, M. / Lang, D. / Thoma, R. / Sterner, R. | ||||||
Citation | Journal: Science / Year: 2000 Title: Structural Evidence for Evolution of the Beta/Alpha-Barrel Scaffold by Repeated Gene Duplication and Fusion Authors: Lang, D. / Thoma, R. / Henn-Sax, M. / Sterner, R. / Wilmanns, M. #1: Journal: FEBS Lett. / Year: 1999 Title: Efficient Expression, Purification and Crystallisation of Two Hyperthermostable Enzymes of Histidine Biosynthesis Authors: Thoma, R. / Obmolova, G. / Lang, D.A. / Schwander, M. / Jenoe, P. / Sterner, R. / Wilmanns, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qo2.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qo2.ent.gz | 91.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qo2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/1qo2 ftp://data.pdbj.org/pub/pdb/validation_reports/qo/1qo2 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9992, -0.01298, -0.03791), Vector: |
-Components
#1: Protein | Mass: 27208.951 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: M1, M17 AND M236 ARE SELENOMETHIONINE SUBSTITUTED / Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Cellular location: CYTOPLASM / Gene: THISA / Plasmid: PDMI, 1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3110 TRPEA2 / References: UniProt: Q9X0C7, D-lyxose ketol-isomerase #2: 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: 1.82 Å3/Da / Density % sol: 31.86 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 Details: SEE THOMA ET AL. (1999) FEBS LETTERS 454, 1-6., pH 5.60 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop / Details: Thoma, R., (1999) FEBS Lett., 454, 1. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.97893, 0.97929, 0.98089 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998 / Details: RHODIUM COATED PRE-MIRROR FOCUSSING MIRROR | ||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.85→39.841 Å / Num. obs: 34932 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 3.51 % / Biso Wilson estimate: 27.24 Å2 / Rsym value: 0.041 / Net I/σ(I): 17 | ||||||||||||
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 1.95 % / Mean I/σ(I) obs: 2.53 / Rsym value: 0.269 / % possible all: 91.9 | ||||||||||||
Reflection | *PLUS Redundancy: 5.8 % / Rmerge(I) obs: 0.048 | ||||||||||||
Reflection shell | *PLUS Rmerge(I) obs: 0.304 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.85→8 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: CNS DEFAULT, ANISOTROPIC B FACTORS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.81 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.87 Å / Total num. of bins used: 34
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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