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- PDB-5t3j: Histidinol Phosphate Phosphatase(HPP) soaked with selenourea for ... -

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Basic information

Entry
Database: PDB / ID: 5t3j
TitleHistidinol Phosphate Phosphatase(HPP) soaked with selenourea for 10 min
ComponentsInositol monophosphatase
KeywordsHYDROLASE / Histidinol Phosphate Phosphatase(HPP) / selenourea
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
PHOSPHATE ION / selenourea / histidinol-phosphatase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsLuo, Z. / Dauter, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Sci Rep / Year: 2016
Title: Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures.
Authors: Luo, Z.
History
DepositionAug 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Refinement description
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 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: Inositol monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6273
Polymers30,4091
Non-polymers2182
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Inositol monophosphatase
hetero molecules

A: Inositol monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2556
Polymers60,8192
Non-polymers4364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area2250 Å2
ΔGint-12 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.635, 119.635, 92.906
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-565-

HOH

21A-576-

HOH

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Components

#1: Protein Inositol monophosphatase / Uncharacterized protein


Mass: 30409.285 Da / Num. of mol.: 1 / Fragment: UNP residues 53-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MTR_3g117220 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD / References: UniProt: G7J7Q5
#2: Chemical ChemComp-SEY / selenourea


Mass: 123.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2Se
#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.: 79 / Source method: isolated from a natural source / Formula: H2O

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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: 3.4 Å3/Da / Density % sol: 63.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% (w/v) PEG 3350, 0.2 M diammonium hydrogen phosphate buffer pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 13333 / % possible obs: 99.9 % / Redundancy: 11.8 % / CC1/2: 0.94 / Rmerge(I) obs: 0.1 / Net I/σ(I): 24.7
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.71 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.55→36.69 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.91 / SU B: 15.829 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.435 / ESU R Free: 0.268
RfactorNum. reflection% reflectionSelection details
Rfree0.23659 1327 10.3 %RANDOM
Rwork0.20377 ---
obs0.20711 11572 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.518 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0.23 Å2-0 Å2
2---0.46 Å2-0 Å2
3---1.48 Å2
Refinement stepCycle: LAST / Resolution: 2.55→36.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 9 79 2078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192045
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9512784
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8635255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.04924.43288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88915324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.365159
X-RAY DIFFRACTIONr_chiral_restr0.1130.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211551
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3392.5071025
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4393.7511279
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1892.6731019
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.47420.8833065
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.548→2.614 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 71 -
Rwork0.309 570 -
obs--66.77 %
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)
11.2755-0.4237-0.30950.3121-0.39622.1252-0.0988-0.0473-0.0119-0.06030.0551-0.07270.356-0.58040.04360.1102-0.09050.00080.3818-0.01690.122210.745545.876967.9257
21.89350.2415-0.29720.5596-0.70534.242-0.04980.04480.0503-0.1551-0.126-0.1402-0.01310.02220.17580.20780.1133-0.03320.07050.00380.089221.990260.940652.7293
31.05440.62780.20081.0595-0.88913.1959-0.0288-0.1502-0.0204-0.1886-0.1386-0.0977-0.1214-0.67660.16740.17430.1943-0.0420.3357-0.03830.074212.198557.868553.3329
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A59 - 190
2X-RAY DIFFRACTION2A191 - 246
3X-RAY DIFFRACTION3A247 - 326

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