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- PDB-5eq8: Crystal structure of Medicago truncatula Histidinol-Phosphate Pho... -

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Basic information

Entry
Database: PDB / ID: 5eq8
TitleCrystal structure of Medicago truncatula Histidinol-Phosphate Phosphatase (MtHPP) in complex with L-histidinol
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 ...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
L-histidinol / histidinol-phosphatase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 1.2Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Assembly

Deposited unit
A: Inositol monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6003
Polymers30,4221
Non-polymers1782
Water5,044280
1
A: Inositol monophosphatase
hetero molecules

A: Inositol monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2006
Polymers60,8452
Non-polymers3554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4110 Å2
ΔGint-42 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.296, 87.296, 61.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

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Components

#1: Protein Inositol monophosphatase


Mass: 30422.305 Da / Num. of mol.: 1
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-HSO / L-histidinol


Type: L-peptide linking / Mass: 142.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12N3O
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 3350, 0.1 M Bis-Tris pH 6.5, 0.2 M ammonium acetate, 10 mM magnesium acetate. Crystals were incubated for 8 min with 5 mM histidinol-phosphate and flash-frozen in Paraton-N

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.7999 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7999 Å / Relative weight: 1
ReflectionResolution: 1.3→40 Å / Num. obs: 59314 / % possible obs: 99.6 % / Redundancy: 16 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 26.5
Reflection shellResolution: 1.3→1.38 Å / Redundancy: 15.4 % / Rmerge(I) obs: 1.359 / Mean I/σ(I) obs: 2.1 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→39.04 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.887 / SU ML: 0.034 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.156 1187 2 %RANDOM
Rwork0.118 ---
obs0.119 58127 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.073 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å2-0 Å2-0 Å2
2--0.83 Å2-0 Å2
3----1.67 Å2
Refinement stepCycle: 1 / Resolution: 1.3→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 11 280 2305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192165
X-RAY DIFFRACTIONr_bond_other_d0.0030.022048
X-RAY DIFFRACTIONr_angle_refined_deg21.9572957
X-RAY DIFFRACTIONr_angle_other_deg1.10734719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7485279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40824.61591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06815342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.418159
X-RAY DIFFRACTIONr_chiral_restr0.120.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022528
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02501
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_it2.8311.7771095
X-RAY DIFFRACTIONr_mcbond_other2.831.7791096
X-RAY DIFFRACTIONr_mcangle_it3.352.6651381
X-RAY DIFFRACTIONr_mcangle_other3.3492.6661382
X-RAY DIFFRACTIONr_scbond_it4.2692.2761069
X-RAY DIFFRACTIONr_scbond_other4.2672.2761070
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9173.2281577
X-RAY DIFFRACTIONr_long_range_B_refined5.16816.8752663
X-RAY DIFFRACTIONr_long_range_B_other4.81215.9592520
X-RAY DIFFRACTIONr_rigid_bond_restr3.8434211
X-RAY DIFFRACTIONr_sphericity_free36.102571
X-RAY DIFFRACTIONr_sphericity_bonded15.02954367
LS refinement shellResolution: 1.3→1.33 Å
RfactorNum. reflection% reflection
Rfree0.305 83 -
Rwork0.253 4045 -
obs--95.18 %

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