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- PDB-9fcg: Medicago truncatula 5'-ProFAR isomerase (HISN3) D57N mutant in co... -

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Basic information

Entry
Database: PDB / ID: 9fcg
TitleMedicago truncatula 5'-ProFAR isomerase (HISN3) D57N mutant in complex with PrFAR
Components1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase, chloroplastic
KeywordsISOMERASE / Complex / product / side-product / BBM II isomerase / histidine biosynthesis / hisA
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 / L-tryptophan biosynthetic process / chloroplast / cytoplasm
Similarity search - Function
His6-like, eukaryotic-type / Histidine biosynthesis, HisA-like / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-2ER / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase, chloroplastic
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsWitek, W. / Imiolczyk, B. / Ruszkowski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreSonata 2018/31/D/NZ1/03630 Poland
CitationJournal: Plant Physiol Biochem. / Year: 2024
Title: Structural, kinetic, and evolutionary peculiarities of HISN3, a plant 5'-ProFAR isomerase.
Authors: Witek, W. / Imiolczyk, B. / Ruszkowski, M.
History
DepositionMay 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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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, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,33710
Polymers29,7111
Non-polymers1,6269
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-67 kcal/mol
Surface area10740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.790, 87.790, 35.633
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Space group name HallP4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 29710.686 Da / Num. of mol.: 1 / Mutation: D57N
Source method: isolated from a genetically manipulated source
Details: Nt42, D57N / Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11441829, MTR_2g015010, MtrunA17_Chr2g0283151 / Production host: Escherichia coli (E. coli)
References: UniProt: G7IFI7, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase

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Non-polymers , 5 types, 313 molecules

#2: Chemical ChemComp-2ER / [(2R,3S,4R,5R)-5-[4-AMINOCARBONYL-5-[[(Z)-[(3R,4R)-3,4-DIHYDROXY-2-OXO-5-PHOSPHONOOXY-PENTYL]IMINOMETHYL]AMINO]IMIDAZOL-1-YL]-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE


Mass: 577.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H25N5O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M sodium bromide, 20% PEG 3350, 1.5 M NaCl in reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.54→80 Å / Num. obs: 40420 / % possible obs: 98.8 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.143 / Rrim(I) all: 0.149 / Net I/σ(I): 12.26
Reflection shellResolution: 1.54→1.63 Å / Rmerge(I) obs: 1.592 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 6090 / CC1/2: 0.598 / Rrim(I) all: 1.677 / % possible all: 92.9

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX1.20.1-4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→35.63 Å / SU ML: 0.1951 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.2023
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1984 1010 2.5 %
Rwork0.1741 39400 -
obs0.1748 40410 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.21 Å2
Refinement stepCycle: LAST / Resolution: 1.54→35.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1971 0 101 304 2376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572105
X-RAY DIFFRACTIONf_angle_d0.90362852
X-RAY DIFFRACTIONf_chiral_restr0.0552323
X-RAY DIFFRACTIONf_plane_restr0.0085358
X-RAY DIFFRACTIONf_dihedral_angle_d13.5214750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.620.31991330.27485199X-RAY DIFFRACTION91.96
1.62-1.720.25061450.21855626X-RAY DIFFRACTION99.98
1.72-1.850.25491450.19255677X-RAY DIFFRACTION99.98
1.85-2.040.20861450.16295638X-RAY DIFFRACTION99.83
2.04-2.330.19491460.15915685X-RAY DIFFRACTION99.98
2.33-2.940.19151460.18045719X-RAY DIFFRACTION99.76
2.94-35.630.17311500.15995856X-RAY DIFFRACTION99.92

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