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- PDB-7bgm: Crystal structure of MtHISN2, a bifunctional enzyme from the hist... -

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Basic information

Entry
Database: PDB / ID: 7bgm
TitleCrystal structure of MtHISN2, a bifunctional enzyme from the histidine biosynthetic pathway
ComponentsPhosphoribosyl-AMP cyclohydrolase
KeywordsHYDROLASE / Histidine / Pyrophosphohydrolase / Cyclohydrolase / Bifunctional / PRA-CH / PRA-PH
Function / homology
Function and homology information


phosphoribosyl-AMP cyclohydrolase activity / phosphoribosyl-ATP diphosphatase activity / L-histidine biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Phosphoribosyl-AMP cyclohydrolase domain / Phosphoribosyl-AMP cyclohydrolase domain superfamily / Phosphoribosyl-AMP cyclohydrolase / Phosphoribosyl-ATP pyrophosphohydrolase / Phosphoribosyl-ATP pyrophosphohydrolase-like / Phosphoribosyl-ATP pyrophosphohydrolase
Similarity search - Domain/homology
Histidine biosynthesis hisIE protein
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsWitek, W. / Ruszkowski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreSONATA 2018/31/D/NZ1/03630 Poland
CitationJournal: Sci Rep / Year: 2021
Title: Structural and mechanistic insights into the bifunctional HISN2 enzyme catalyzing the second and third steps of histidine biosynthesis in plants.
Authors: Witek, W. / Sliwiak, J. / Ruszkowski, M.
History
DepositionJan 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosyl-AMP cyclohydrolase
B: Phosphoribosyl-AMP cyclohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,97311
Polymers53,3842
Non-polymers5899
Water6,413356
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-353 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.422, 69.477, 52.130
Angle α, β, γ (deg.)90.000, 94.696, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-423-

HOH

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Components

#1: Protein Phosphoribosyl-AMP cyclohydrolase


Mass: 26692.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Without a signal peptide (residues 1-48) / Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 25498966, MTR_7g084480, MtrunA17_Chr7g0252441 / Plasmid: pMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A072U2X9, phosphoribosyl-AMP cyclohydrolase, phosphoribosyl-ATP diphosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.27 Å3/Da / Density % sol: 62.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol) 0.1 M Buffer System 1 , pH 6.5 (Imidazole; MES-acid) ...Details: 0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol) 0.1 M Buffer System 1 , pH 6.5 (Imidazole; MES-acid) 30% Precipitant Mix 1 (20% v/v PEG 500* MME; 10 % w/v PEG 20000. Cryoprotection: 20% ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→80 Å / Num. obs: 79751 / % possible obs: 98.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 25.3 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.6
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 12569 / CC1/2: 0.69 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Cootmodel building
PHENIXAutobuildmodel building
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→42.93 Å / SU ML: 0.155 / Cross valid method: FREE R-VALUE / Phase error: 18.9436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1747 1037 1.3 %
Rwork0.1434 78701 -
obs0.1439 79738 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.58 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3336 0 9 356 3701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01063381
X-RAY DIFFRACTIONf_angle_d1.01384571
X-RAY DIFFRACTIONf_chiral_restr0.0589539
X-RAY DIFFRACTIONf_plane_restr0.0063582
X-RAY DIFFRACTIONf_dihedral_angle_d14.70731250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.680.27261440.213410926X-RAY DIFFRACTION95.92
1.68-1.790.20541480.168911242X-RAY DIFFRACTION98.91
1.79-1.930.20821480.148911278X-RAY DIFFRACTION99.12
1.93-2.120.19281480.127711234X-RAY DIFFRACTION99.15
2.12-2.430.16171490.126311259X-RAY DIFFRACTION98.92
2.43-3.060.1731490.149711323X-RAY DIFFRACTION98.86
3.06-42.930.16261510.141511439X-RAY DIFFRACTION98.72

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