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- PDB-5eq7: Crystal structure of Medicago truncatula Histidinol-Phosphate Pho... -

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Basic information

Entry
Database: PDB / ID: 5eq7
TitleCrystal structure of Medicago truncatula Histidinol-Phosphate Phosphatase (MtHPP) in complex with free phosphate
ComponentsInositol monophosphatase
KeywordsBIOSYNTHETIC PROTEIN / histidine biosynthesis / metabolic pathways / dimer / plant
Function / homology
Function and homology information


histidinol-phosphatase activity / histidinol-phosphatase / 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
PHOSPHATE ION / histidinol-phosphatase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 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 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / 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)30,5533
Polymers30,4221
Non-polymers1302
Water5,603311
1
A: Inositol monophosphatase
hetero molecules

A: Inositol monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1056
Polymers60,8452
Non-polymers2614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3470 Å2
ΔGint-49 kcal/mol
Surface area20480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.980, 86.980, 61.850
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-514-

HOH

21A-765-

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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 1.92 Å3/Da / Density % sol: 36.03 %
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. Paraton-N as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.992 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 1.19→40 Å / Num. obs: 76240 / % possible obs: 99.9 % / Redundancy: 34.3 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 24.7
Reflection shellResolution: 1.19→1.22 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4n81

4n81


Resolution: 1.19→38.9 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.045 / SU ML: 0.021 / Cross valid method: FREE R-VALUE / ESU R: 0.028 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14 1144 1.5 %RANDOM
Rwork0.11 ---
obs0.111 75096 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.039 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å2-0 Å2-0 Å2
2--0.53 Å2-0 Å2
3----1.06 Å2
Refinement stepCycle: 1 / Resolution: 1.19→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 6 311 2323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192154
X-RAY DIFFRACTIONr_bond_other_d0.0010.022037
X-RAY DIFFRACTIONr_angle_refined_deg2.11.9552945
X-RAY DIFFRACTIONr_angle_other_deg1.51334695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4255279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72224.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79715341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.586159
X-RAY DIFFRACTIONr_chiral_restr0.1530.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022493
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02494
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_it5.3311.3011092
X-RAY DIFFRACTIONr_mcbond_other5.3331.2991091
X-RAY DIFFRACTIONr_mcangle_it5.2781.9471379
X-RAY DIFFRACTIONr_mcangle_other5.2771.9481380
X-RAY DIFFRACTIONr_scbond_it5.931.871062
X-RAY DIFFRACTIONr_scbond_other5.9111.8641058
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9772.5691560
X-RAY DIFFRACTIONr_long_range_B_refined7.10313.8212741
X-RAY DIFFRACTIONr_long_range_B_other6.62212.7142561
X-RAY DIFFRACTIONr_rigid_bond_restr11.65134190
X-RAY DIFFRACTIONr_sphericity_free49.914568
X-RAY DIFFRACTIONr_sphericity_bonded16.25954383
LS refinement shellResolution: 1.19→1.22 Å
RfactorNum. reflection% reflection
Rfree0.236 82 -
Rwork0.233 5421 -
obs--99.1 %

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