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Open data
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Basic information
Entry | Database: PDB / ID: 5g4e | ||||||
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Title | S. enterica HisA mutant D10G, Dup13-15, Q24L, G102A, V106L | ||||||
![]() | 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase | ||||||
![]() | ISOMERASE / HISA / PROTEIN EVOLUTION / IAD MODEL / TRPF | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Soderholm, A. / Guo, X. / Newton, M. / Nasvall, J. / Duarte, F. / Andersson, D. / Patrick, W. / Selmer, M. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.4 KB | Display | ![]() |
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PDB format | ![]() | 71.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481.7 KB | Display | ![]() |
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Full document | ![]() | 487.1 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
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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.) ![]() 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: ![]() ![]() 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 ![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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