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- PDB-7zgh: Crystal Structure of Amycolatopsis jejuensis Multiple Inositol Po... -

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Basic information

Entry
Database: PDB / ID: 7zgh
TitleCrystal Structure of Amycolatopsis jejuensis Multiple Inositol Polyphosphate Phosphatase, complex with myo-inositol hexakissulfate
ComponentsMultiple inositol-polyphosphate phosphatase
KeywordsHYDROLASE / phytase / histidine phosphatase / MINPP / Amycolatopsis
Function / homologyPhosphoglycerate mutase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / D-MYO-INOSITOL-HEXASULPHATE
Function and homology information
Biological speciesAmycolatopsis jejuensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsAcquistapace, I.M. / Brearley, C.A. / Hemmings, A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M022978/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal Structure of Amycolatopsis jejuensis Multiple Inositol Polyphosphate Phosphatase, complex with myo-inositol hexakissulfate
Authors: Acquistapace, I.M. / Brearley, C.A. / Hemmings, A.M.
History
DepositionApr 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multiple inositol-polyphosphate phosphatase
B: Multiple inositol-polyphosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2496
Polymers93,7432
Non-polymers1,5054
Water14,700816
1
A: Multiple inositol-polyphosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7164
Polymers46,8721
Non-polymers8453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Multiple inositol-polyphosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5322
Polymers46,8721
Non-polymers6611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.840, 86.420, 70.110
Angle α, β, γ (deg.)90.000, 98.290, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Multiple inositol-polyphosphate phosphatase


Mass: 46871.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis jejuensis (bacteria) / Gene: GFH48_35735 / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle Express T7 / References: multiple inositol-polyphosphate phosphatase
#2: Chemical ChemComp-IHS / D-MYO-INOSITOL-HEXASULPHATE


Mass: 660.535 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O24S6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 816 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M Lithium sulfate, 0.1 M Phosphate/citrate, 20 % w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.41→32.192 Å / Num. obs: 152343 / % possible obs: 99.08 % / Redundancy: 4.3 % / Biso Wilson estimate: 14.39 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.036 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
1.41-1.432.850.8251.267320.5360.55688.39
1.43-1.463.120.8111.373090.5640.51895.38
1.46-1.493.670.7641.676490.6420.45199.77
1.49-1.524.010.652276490.7270.36999.78
1.52-1.554.480.62.476710.80.31699.88
1.55-1.594.540.5082.876560.8370.26699.9
1.59-1.634.490.4333.376790.880.22899.81
1.63-1.674.390.3563.876590.19199.95
1.67-1.724.560.3084.576190.9330.1699.9
1.72-1.784.450.2615.276820.9480.13999.9
1.78-1.844.630.2146.577190.9660.11199.9
1.84-1.914.550.1698.176270.9780.08999.88
1.91-24.450.1369.876980.9840.07399.87
2-2.114.470.10712.476680.9890.05799.91
2.11-2.244.620.08416.176760.9930.04499.93
2.24-2.414.580.0718.977090.9950.03799.91
2.41-2.654.570.05822.177040.9960.0399.92
2.65-3.044.590.04727.777070.9980.02499.91
3.04-3.834.530.03239.577320.9990.01799.9
3.83-32.24.410.02648.478340.9990.01499.81

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Processing

Software
NameVersionClassification
GDAdata collection
PHENIX1.19.2_4158refinement
xia2data reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RXD

6rxd


Resolution: 1.41→32.19 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2616
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1831 7714 5.06 %
Rwork0.149 144595 -
obs0.1507 152309 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.07 Å2
Refinement stepCycle: LAST / Resolution: 1.41→32.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6542 0 84 816 7442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00596912
X-RAY DIFFRACTIONf_angle_d0.86079419
X-RAY DIFFRACTIONf_chiral_restr0.0811000
X-RAY DIFFRACTIONf_plane_restr0.00791242
X-RAY DIFFRACTIONf_dihedral_angle_d8.1783993
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.430.31212120.26974207X-RAY DIFFRACTION87.21
1.43-1.440.31862390.25744461X-RAY DIFFRACTION91.83
1.44-1.460.31212340.24374685X-RAY DIFFRACTION96.56
1.46-1.480.25072520.22684837X-RAY DIFFRACTION99.86
1.48-1.50.2362480.20934848X-RAY DIFFRACTION99.69
1.5-1.520.22292830.19754792X-RAY DIFFRACTION99.72
1.52-1.540.23212660.19084874X-RAY DIFFRACTION99.88
1.54-1.560.20912680.18824826X-RAY DIFFRACTION99.86
1.56-1.590.22322530.17694839X-RAY DIFFRACTION99.92
1.59-1.610.23132940.17044843X-RAY DIFFRACTION99.77
1.61-1.640.22252590.16164835X-RAY DIFFRACTION99.88
1.64-1.670.19092610.15034845X-RAY DIFFRACTION99.96
1.67-1.70.19442440.14884849X-RAY DIFFRACTION99.82
1.7-1.740.19042550.1494880X-RAY DIFFRACTION99.81
1.74-1.780.18782900.13974781X-RAY DIFFRACTION99.92
1.78-1.820.17962750.13774817X-RAY DIFFRACTION99.88
1.82-1.860.17892670.13774874X-RAY DIFFRACTION99.84
1.86-1.910.18722510.13924861X-RAY DIFFRACTION99.92
1.91-1.970.17932900.13234830X-RAY DIFFRACTION99.84
1.97-2.030.17382880.13154817X-RAY DIFFRACTION99.9
2.03-2.110.16482580.13124881X-RAY DIFFRACTION99.88
2.11-2.190.18032320.12934908X-RAY DIFFRACTION99.9
2.19-2.290.15662430.12574861X-RAY DIFFRACTION99.94
2.29-2.410.17162430.13354895X-RAY DIFFRACTION99.88
2.41-2.560.16622570.14184861X-RAY DIFFRACTION99.98
2.56-2.760.18462210.14754904X-RAY DIFFRACTION99.79
2.76-3.040.16712780.14624886X-RAY DIFFRACTION99.92
3.04-3.480.17322790.14234877X-RAY DIFFRACTION99.88
3.48-4.380.16232310.13464934X-RAY DIFFRACTION99.83
4.38-32.190.17172430.15864987X-RAY DIFFRACTION99.58

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