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- PDB-2agk: Structure of S. cerevisiae His6 protein -

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Basic information

Entry
Database: PDB / ID: 2agk
TitleStructure of S. cerevisiae His6 protein
Components1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
KeywordsISOMERASE / TIM alpha/beta barrel / Structural Genomics / S. cerevisiae structural genomics project / Paris-Sud Yeast Structural Genomics / YSG
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 / nucleus / cytoplasm
Similarity search - Function
His6-like, eukaryotic-type / Histidine biosynthesis, HisA-like / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsTilbeurgh, H.V. / Paris-Sud Yeast Structural Genomics (YSG)
CitationJournal: Protein Sci. / Year: 2006
Title: Crystal structure of the yeast His6 enzyme suggests a reaction mechanism
Authors: Quevillon-Cheruel, S. / Leulliot, N. / Graille, M. / Blondeau, K. / Janin, J. / Tilbeurgh, H.V.
History
DepositionJul 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8796
Polymers29,4651
Non-polymers4145
Water6,197344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.863, 71.427, 40.570
Angle α, β, γ (deg.)90.00, 104.71, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1349-

HOH

DetailsThe biological assembly is the monomer of the asymmetric unit.

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Components

#1: Protein 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase / Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase / 5-proFAR isomerase


Mass: 29465.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YIL020c / Production host: Escherichia coli (E. coli)
References: UniProt: P40545, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG4000, sodium citrate, MgCl2, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 14, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.25→20 Å / Num. all: 293459 / Num. obs: 270881 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.89
Reflection shellResolution: 1.25→1.3 Å / % possible obs: 88.1 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.85 / Num. measured obs: 28819 / Num. unique obs: 7572 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.729 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 3307 5 %RANDOM
Rwork0.191 ---
all0.193 ---
obs-65836 95.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å2-0.95 Å2
2---0.29 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 26 344 2246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221943
X-RAY DIFFRACTIONr_angle_refined_deg1.1171.9552612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1095230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.87424.79296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47115353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0491510
X-RAY DIFFRACTIONr_chiral_restr0.0820.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021450
X-RAY DIFFRACTIONr_nbd_refined0.1880.2917
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21322
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.242
X-RAY DIFFRACTIONr_mcbond_it1.0141.51181
X-RAY DIFFRACTIONr_mcangle_it1.60221838
X-RAY DIFFRACTIONr_scbond_it4.5663878
X-RAY DIFFRACTIONr_scangle_it3.9514.5774
X-RAY DIFFRACTIONr_rigid_bond_restr5.38232059
X-RAY DIFFRACTIONr_sphericity_free2.6163345
X-RAY DIFFRACTIONr_sphericity_bonded3.0831910
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 234 -
Rwork0.3 4670 -
all-4904 -
obs--97.09 %

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