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- PDB-5eq9: Crystal structure of Medicago truncatula Histidinol-Phosphate Pho... -

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Basic information

Entry
Database: PDB / ID: 5eq9
TitleCrystal structure of Medicago truncatula Histidinol-Phosphate Phosphatase (MtHPP) in complex with L-histidinol phosphate and Mg2+
ComponentsInositol monophosphatase
KeywordsBIOSYNTHETIC PROTEIN / histidine biosynthesis / metabolic pathways / dimer / plant
Function / homology
Function and homology information


histidinol-phosphatase / histidinol-phosphatase activity / L-histidine biosynthetic process / metal ion binding
Similarity search - Function
Histidinol-phosphate phosphatase, putative, inositol monophosphatase / Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich ...Histidinol-phosphate phosphatase, putative, inositol monophosphatase / Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HSA / histidinol-phosphatase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsRuszkowski, M. / Dauter, Z.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Studies of Medicago truncatula Histidinol Phosphate Phosphatase from Inositol Monophosphatase Superfamily Reveal Details of Penultimate Step of Histidine Biosynthesis in Plants.
Authors: Ruszkowski, M. / Dauter, Z.
History
DepositionNov 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol monophosphatase
B: Inositol monophosphatase
C: Inositol monophosphatase
D: Inositol monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,71113
Polymers121,6374
Non-polymers1,0749
Water23,6901315
1
A: Inositol monophosphatase
B: Inositol monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3096
Polymers60,8192
Non-polymers4914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-29 kcal/mol
Surface area20300 Å2
MethodPISA
2
C: Inositol monophosphatase
D: Inositol monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4027
Polymers60,8192
Non-polymers5835
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-29 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.885, 89.802, 92.593
Angle α, β, γ (deg.)90.00, 97.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Inositol monophosphatase


Mass: 30409.285 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MTR_3g117220 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: G7J7Q5
#2: Chemical
ChemComp-HSA / PHOSPHORIC ACID MONO-[2-AMINO-3-(3H-IMIDAZOL-4-YL)-PROPYL]ESTER


Mass: 221.151 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12N3O4P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1315 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein at 19 mg/ml concentration. 15% PEG 3350, 0.2 M diammonium hydrogen phosphate, pH 8.0. Crystal washed in a crystallization solution supplemented with 2 mM MgCl2, 5 mM HOLP and 20% ...Details: Protein at 19 mg/ml concentration. 15% PEG 3350, 0.2 M diammonium hydrogen phosphate, pH 8.0. Crystal washed in a crystallization solution supplemented with 2 mM MgCl2, 5 mM HOLP and 20% glycerol and immediately vitrified in liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.36→40 Å / Num. obs: 214644 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 15
Reflection shellResolution: 1.36→1.44 Å / Redundancy: 5 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.9 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→36.25 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.922 / SU ML: 0.033 / Cross valid method: FREE R-VALUE / ESU R: 0.043 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.156 1074 0.5 %RANDOM
Rwork0.116 ---
obs0.116 213570 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.576 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20.81 Å2
2--0.04 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.36→36.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7967 0 66 1315 9348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0198262
X-RAY DIFFRACTIONr_bond_other_d0.0020.027817
X-RAY DIFFRACTIONr_angle_refined_deg1.91.95811259
X-RAY DIFFRACTIONr_angle_other_deg1.112317996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29351040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72924.507355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.056151331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1611536
X-RAY DIFFRACTIONr_chiral_restr0.1370.21272
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219365
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021889
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2961.3264126
X-RAY DIFFRACTIONr_mcbond_other2.2961.3264126
X-RAY DIFFRACTIONr_mcangle_it2.9091.9935143
X-RAY DIFFRACTIONr_mcangle_other2.9091.9935144
X-RAY DIFFRACTIONr_scbond_it3.9491.7694136
X-RAY DIFFRACTIONr_scbond_other3.9481.7694136
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7692.4846106
X-RAY DIFFRACTIONr_long_range_B_refined5.78413.78210537
X-RAY DIFFRACTIONr_long_range_B_other5.78413.78310538
X-RAY DIFFRACTIONr_rigid_bond_restr3.702316079
X-RAY DIFFRACTIONr_sphericity_free39.4995303
X-RAY DIFFRACTIONr_sphericity_bonded14.752516921
LS refinement shellResolution: 1.36→1.4 Å
RfactorNum. reflection% reflection
Rfree0.346 78 -
Rwork0.265 15365 -
obs--97.6 %

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