+Open data
-Basic information
Entry | Database: PDB / ID: 5g4e | ||||||
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Title | S. enterica HisA mutant D10G, Dup13-15, Q24L, G102A, V106L | ||||||
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: 2.65 Å | ||||||
Authors | Soderholm, A. / Guo, X. / Newton, M. / Nasvall, J. / Duarte, F. / Andersson, D. / Patrick, W. / 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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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g4e.cif.gz | 94.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g4e.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 5g4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g4e_validation.pdf.gz | 481.7 KB | Display | wwPDB validaton report |
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Full document | 5g4e_full_validation.pdf.gz | 487.1 KB | Display | |
Data in XML | 5g4e_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 5g4e_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/5g4e ftp://data.pdbj.org/pub/pdb/validation_reports/g4/5g4e | HTTPS FTP |
-Related structure data
Related structure data | 5ab3C 5ac7C 5ac8C 5g1tSC 5g1yC 5g2hC 5g2iC 5g2wC 5g4wC 5g5iC 5l6uC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27442.430 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica (bacteria) Gene: hisA, AIY46_13150, AL463_17045, CQW68_13095, D3346_17640, D3Q81_15095, EAW95_14430, FJR52_10950, GCH85_22590, NCTC6385_02080, ND68_15100 Plasmid: PEXP5-CT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0A630AQ07, UniProt: P10372*PLUS, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase |
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-Non-polymers , 5 types, 35 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | #5: Chemical | ChemComp-GOL / | #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: 47 % / Description: NONE |
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Crystal grow | pH: 5.2 Details: 0.18 M AMMONIUM ACETATE, 0.09 M SODIUM ACETATE, PH 5.15, 27% W/V PEG4000 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Detector: CCD / Date: Apr 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 19821 / % possible obs: 95.2 % / Observed criterion σ(I): 1.6 / Redundancy: 4.1 % / Biso Wilson estimate: 34.87 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 4 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.7 / % possible all: 80.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5G1T Resolution: 2.65→45.097 Å / SU ML: 0.33 / σ(F): 1.35 / Phase error: 33.7 / Stereochemistry target values: ML Details: RESIDUES 138-141 IN CHAIN A WERE MODELED AS ALA DUE TO LACK OF ELECTRON DENSITY FOR SIDE CHAINS. THE REGISTER OF THIS REGION IS AMBIGUOUS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→45.097 Å
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Refine LS restraints |
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LS refinement shell |
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