+Open data
-Basic information
Entry | Database: PDB / ID: 5l6u | ||||||
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Title | S. ENTERICA HISA MUTANT - D10G, DUP13-15, Q24L, G102A | ||||||
Components | 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase | ||||||
Keywords | ISOMERASE / HisA / protein evolution / IAD model / TrpF | ||||||
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 | Salmonella enterica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Guo, X. / Soderholm, A. / Selmer, M. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Structural and functional innovations in the real-time evolution of new ( beta alpha )8 barrel enzymes. Authors: Newton, M.S. / Guo, X. / Soderholm, A. / Nasvall, J. / Lundstrom, P. / Andersson, D.I. / Selmer, M. / Patrick, W.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l6u.cif.gz | 112 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l6u.ent.gz | 85.7 KB | Display | PDB format |
PDBx/mmJSON format | 5l6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/5l6u ftp://data.pdbj.org/pub/pdb/validation_reports/l6/5l6u | HTTPS FTP |
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-Related structure data
Related structure data | 5ab3C 5ac7C 5ac8C 5g1tSC 5g1yC 5g2hC 5g2iC 5g2wC 5g4eC 5g4wC 5g5iC 5l9fC 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27504.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CYS241 is partially modified to CME / Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: hisA, SeHA_C2302 / Plasmid: pEXP5-CT / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B4T9N8, UniProt: P10372*PLUS, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 0.2M ammonium sulfate, 0.1M sodium acetate, pH4.8, 25% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97628 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97628 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→74.426 Å / Num. obs: 35410 / % possible obs: 99.8 % / Redundancy: 38.4 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.084 / Net I/σ(I): 37 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 39 % / Rmerge(I) obs: 1.62 / Mean I/σ(I) obs: 2.77 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5g1t Resolution: 1.6→74.426 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→74.426 Å
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Refine LS restraints |
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LS refinement shell |
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