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

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Basic information

Entry
Database: PDB / ID: 9fcf
TitleMedicago truncatula 5'-ProFAR isomerase (HISN3) D57N mutant in complex with ProFAR
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 / 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-GUO / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase HISN3, chloroplastic
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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

Downloads & links

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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)30,3464
Polymers29,7111
Non-polymers6363
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-24 kcal/mol
Surface area11370 Å2
Unit cell
Length a, b, c (Å)91.301, 91.301, 35.836
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

#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
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
#2: Chemical ChemComp-GUO / [(2R,3S,4R,5R)-5-[4-aminocarbonyl-5-[(E)-[[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]amino]methylideneamino]imidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate


Mass: 577.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25N5O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M sodium acetate, 0.1 M sodium cacodylate pH 6.5, 15% PEG 8000

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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: 2.36→80 Å / Num. obs: 12535 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 39.94 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.16 / Net I/σ(I): 10.74
Reflection shellResolution: 2.36→2.5 Å / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 1978 / CC1/2: 0.842 / Rrim(I) all: 1.024

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→32.28 Å / SU ML: 0.3863 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.2882
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2569 1000 7.99 %
Rwork0.2238 11522 -
obs0.2265 12522 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.73 Å2
Refinement stepCycle: LAST / Resolution: 2.36→32.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 39 4 2067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522096
X-RAY DIFFRACTIONf_angle_d0.82122838
X-RAY DIFFRACTIONf_chiral_restr0.0548325
X-RAY DIFFRACTIONf_plane_restr0.0068362
X-RAY DIFFRACTIONf_dihedral_angle_d14.1449757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.480.44081400.36671617X-RAY DIFFRACTION100
2.48-2.640.35241410.32091623X-RAY DIFFRACTION99.89
2.64-2.840.3191420.29811635X-RAY DIFFRACTION99.78
2.84-3.120.321410.28771620X-RAY DIFFRACTION99.77
3.13-3.580.26191430.22971651X-RAY DIFFRACTION99.89
3.58-4.50.22431450.17461659X-RAY DIFFRACTION99.72
4.51-32.280.18951480.16931717X-RAY DIFFRACTION99.89
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.25180277944-0.459039391784-1.212009619830.475950117870.1209981238941.88788112894-0.316892396395-0.00460569458270.0715532829975-0.2003451742280.04671940311340.0369368470826-0.213217313876-0.1244775047210.2947575846770.350677680003-0.0170984623768-0.1118927678180.2226748906270.07444821530630.51308238587816.809593609919.5722726122-3.78967765746
20.8662209479090.1172646923930.2482967712851.055139549140.2295580667151.23327383576-0.04356559120740.02696113000330.1741387608060.000136187632307-0.0882664869996-0.085167966455-0.153669665139-0.0008607117960660.0665307968330.396574100176-0.0301204731229-0.1529414561160.3649209106450.1390065993060.58379284794416.814042866426.5773552046-0.376107121743
33.615742745361.477329089994.760203931872.21382346713.134088072477.550215814240.3015429990120.92865173671-0.3313624564320.597339550442-0.270124964649-0.1648073590471.120804117410.892838166076-0.2478090489250.3977978191550.0496539504918-0.1437778421090.5092868320260.22530306410.59838954216633.006873208112.9481956164.08411638538
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 42 through 83 )42 - 831 - 36
22chain 'A' and (resid 84 through 296 )84 - 29637 - 249
33chain 'A' and (resid 297 through 312 )297 - 312250 - 265

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