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

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Basic information

Entry
Database: PDB / ID: 7zgg
TitleCrystal Structure of Amycolatopsis jejuensis Multiple Inositol Polyphosphate Phosphatase, phosphate-bound
ComponentsMultiple inositol-polyphosphate phosphatase
KeywordsHYDROLASE / phytase / histidine phosphatase / MINPP / Amycolatopsis
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesAmycolatopsis jejuensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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, apo-protein
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

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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)94,0255
Polymers93,7432
Non-polymers2823
Water15,475859
1
A: Multiple inositol-polyphosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0593
Polymers46,8721
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Multiple inositol-polyphosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9672
Polymers46,8721
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.887, 86.910, 70.540
Angle α, β, γ (deg.)90.000, 97.928, 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) / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle Express T7 / References: EC: 3.1.3.62
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 859 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.28 % / Description: plate clusters
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M NaThiocyanate, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.659→69.93 Å / Num. obs: 97117 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 13.12 Å2 / Rrim(I) all: 0.19 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 2 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.66-1.721.151196790.2151.62799.5
1.72-1.790.9041.396420.3121.27999.9
1.79-1.870.6371.897000.4690.901100
1.87-1.970.4352.597110.650.615100
1.97-2.090.3093.496760.780.43799.9
2.09-2.250.2174.696700.8740.30799.9
2.25-2.480.1556.297220.9310.219100
2.48-2.840.11897380.9630.156100
2.84-3.570.05913.297470.990.083100
3.57-69.930.02721.898920.9980.039100

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Processing

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

6rxd


Resolution: 1.66→69.87 Å / SU ML: 0.2629 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.4488
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2263 4698 4.85 %
Rwork0.1801 92217 -
obs0.1824 96915 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.76 Å2
Refinement stepCycle: LAST / Resolution: 1.66→69.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 0 16 859 7409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00736720
X-RAY DIFFRACTIONf_angle_d0.87559117
X-RAY DIFFRACTIONf_chiral_restr0.0516970
X-RAY DIFFRACTIONf_plane_restr0.00821208
X-RAY DIFFRACTIONf_dihedral_angle_d5.6302923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.680.37711790.33643012X-RAY DIFFRACTION97.67
1.68-1.70.34521380.32533044X-RAY DIFFRACTION99.13
1.7-1.720.36511500.30213073X-RAY DIFFRACTION99.17
1.72-1.740.41881400.30923022X-RAY DIFFRACTION99.4
1.74-1.760.39031590.28433097X-RAY DIFFRACTION99.51
1.76-1.790.37021460.2743032X-RAY DIFFRACTION99.41
1.79-1.810.32921600.26763093X-RAY DIFFRACTION99.36
1.81-1.840.30641700.25142989X-RAY DIFFRACTION99.81
1.84-1.870.27961640.22053084X-RAY DIFFRACTION99.57
1.87-1.90.30421410.21523074X-RAY DIFFRACTION99.78
1.9-1.930.28321500.20723047X-RAY DIFFRACTION99.47
1.93-1.970.27981360.23136X-RAY DIFFRACTION99.79
1.97-2.010.26191640.19533030X-RAY DIFFRACTION99.87
2.01-2.050.25011700.19743053X-RAY DIFFRACTION99.75
2.05-2.090.25781640.19573078X-RAY DIFFRACTION99.63
2.09-2.140.2451450.17113073X-RAY DIFFRACTION99.69
2.14-2.190.20411550.16573052X-RAY DIFFRACTION99.84
2.19-2.250.19931610.15623072X-RAY DIFFRACTION99.91
2.25-2.320.2161660.1563053X-RAY DIFFRACTION99.94
2.32-2.390.21241490.15573131X-RAY DIFFRACTION99.88
2.39-2.480.22151390.15393072X-RAY DIFFRACTION99.84
2.48-2.580.23651550.15093092X-RAY DIFFRACTION99.91
2.58-2.70.1861710.15063068X-RAY DIFFRACTION99.78
2.7-2.840.2131260.14833116X-RAY DIFFRACTION99.88
2.84-3.020.17871380.15263105X-RAY DIFFRACTION99.94
3.02-3.250.181720.14823093X-RAY DIFFRACTION99.97
3.25-3.570.16611540.1473079X-RAY DIFFRACTION99.91
3.57-4.090.1611940.14133080X-RAY DIFFRACTION99.94
4.09-5.160.19471670.15493104X-RAY DIFFRACTION99.97
5.16-69.870.21191750.18883163X-RAY DIFFRACTION99.76

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