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- PDB-7r5y: Crystal Structure of Prevotella sp. CAG:617 Multiple Inositol Pol... -

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Basic information

Entry
Database: PDB / ID: 7r5y
TitleCrystal Structure of Prevotella sp. CAG:617 Multiple Inositol Polyphosphate Phosphatase, complex with myo-inositol hexakissulfate
ComponentsHistidine acid phosphatase
KeywordsHYDROLASE / phytase / histidine phosphatase / MINPP / Prevotella
Function / homologyHistidine phosphatase superfamily / D-MYO-INOSITOL-HEXASULPHATE / Histidine acid phosphatase
Function and homology information
Biological speciesPrevotella sp. CAG:617 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 Prevotella sp. CAG:617 Multiple Inositol Polyphosphate Phosphatase, complex with myo-inositol hexakissulfate
Authors: Acquistapace, I.M. / Brearley, C.A. / Hemmings, A.M.
History
DepositionFeb 12, 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

Downloads & links

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Assembly

Deposited unit
A: Histidine acid phosphatase
B: Histidine acid phosphatase
C: Histidine acid phosphatase
D: Histidine acid phosphatase
E: Histidine acid phosphatase
F: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,50113
Polymers285,4426
Non-polymers4,0597
Water35,6881981
1
A: Histidine acid phosphatase
hetero molecules

E: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5645
Polymers95,1472
Non-polymers1,4173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3510 Å2
ΔGint-30 kcal/mol
Surface area33570 Å2
MethodPISA
2
B: Histidine acid phosphatase
F: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4684
Polymers95,1472
Non-polymers1,3212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-19 kcal/mol
Surface area33290 Å2
MethodPISA
3
C: Histidine acid phosphatase
D: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4684
Polymers95,1472
Non-polymers1,3212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-19 kcal/mol
Surface area33320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.140, 263.630, 85.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

#1: Protein
Histidine acid phosphatase


Mass: 47573.652 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prevotella sp. CAG:617 (bacteria) / Gene: BN736_00172 / Production host: Escherichia coli (E. coli) / Variant (production host): Shuffle Express T7 / References: UniProt: R7PD89
#2: Chemical
ChemComp-IHS / D-MYO-INOSITOL-HEXASULPHATE


Mass: 660.535 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H12O24S6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1981 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.1M NaCl, 30% w/v polypropylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.97→73.37 Å / Num. obs: 230183 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 32.38 Å2 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.068 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
1.97-26.81.561.2114090.5580.64799.9
2-2.046.721.3991.4113700.5970.58499.98
2.04-2.086.461.1521.7114280.6850.492100
2.08-2.126.631.0051.005114080.7510.423100
2.12-2.176.790.9152.3113950.790.38199.99
2.17-2.226.670.7632.7114120.8380.32199.96
2.22-2.276.330.643.2114490.8690.278100
2.27-2.346.80.6163.7114150.8980.25899.99
2.34-2.46.710.5374.2114380.910.226100
2.4-2.486.670.4874.8114360.9320.20699.98
2.48-2.576.390.455.4114430.9430.194100
2.57-2.676.690.3836.4114740.960.161100
2.67-2.86.710.3077.8114930.9740.129100
2.8-2.946.560.2369.4114880.9810.1100
2.94-3.136.810.17911.6115180.9880.075100
3.13-3.376.530.13413.8115580.9910.05799.98
3.37-3.716.360.116.4115630.9930.04399.93
3.71-4.246.270.08518.7116280.9930.03799.97
4.24-5.356.330.07320.5117150.9950.03199.93
5.35-73.426.170.0621.3121430.9970.026100

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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: 4tsr

4tsr


Resolution: 1.97→73.37 Å / SU ML: 0.2764 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4542
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2195 11677 5.08 %
Rwork0.1517 218334 -
obs0.1551 230011 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.63 Å2
Refinement stepCycle: LAST / Resolution: 1.97→73.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19846 0 221 1981 22048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006920588
X-RAY DIFFRACTIONf_angle_d0.852127986
X-RAY DIFFRACTIONf_chiral_restr0.05072975
X-RAY DIFFRACTIONf_plane_restr0.00763585
X-RAY DIFFRACTIONf_dihedral_angle_d8.17092908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-1.990.37023900.30127227X-RAY DIFFRACTION99.9
1.99-2.020.33433750.26917233X-RAY DIFFRACTION99.96
2.02-2.040.33823870.24717155X-RAY DIFFRACTION99.95
2.04-2.070.3263990.22517232X-RAY DIFFRACTION99.91
2.07-2.090.28493900.227175X-RAY DIFFRACTION99.93
2.09-2.120.28133730.20397249X-RAY DIFFRACTION99.95
2.12-2.150.2853820.20437187X-RAY DIFFRACTION99.92
2.15-2.180.28223880.20687250X-RAY DIFFRACTION99.95
2.18-2.220.29933580.20337230X-RAY DIFFRACTION99.89
2.22-2.260.28883820.19287201X-RAY DIFFRACTION99.95
2.26-2.290.2793580.19377310X-RAY DIFFRACTION99.93
2.29-2.340.27513780.19377221X-RAY DIFFRACTION99.95
2.34-2.380.28894100.18967175X-RAY DIFFRACTION99.95
2.38-2.430.29633880.18457299X-RAY DIFFRACTION99.92
2.43-2.480.2694000.16337191X-RAY DIFFRACTION99.97
2.48-2.540.23413960.14457217X-RAY DIFFRACTION99.96
2.54-2.60.23074090.14227207X-RAY DIFFRACTION99.97
2.6-2.670.2143700.14287308X-RAY DIFFRACTION99.96
2.67-2.750.22823800.14127293X-RAY DIFFRACTION100
2.75-2.840.22044130.14947236X-RAY DIFFRACTION99.99
2.84-2.940.2393860.15767267X-RAY DIFFRACTION100
2.94-3.060.23243350.15327350X-RAY DIFFRACTION99.96
3.06-3.20.22873820.15357271X-RAY DIFFRACTION99.95
3.2-3.370.23634110.15157318X-RAY DIFFRACTION99.96
3.37-3.580.21114040.14317294X-RAY DIFFRACTION99.94
3.58-3.860.17114020.12157342X-RAY DIFFRACTION99.85
3.86-4.240.16413810.11127356X-RAY DIFFRACTION99.94
4.24-4.860.15374040.1037374X-RAY DIFFRACTION99.79
4.86-6.120.18084000.12827464X-RAY DIFFRACTION99.95
6.12-73.370.1854460.15187702X-RAY DIFFRACTION99.51

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