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- PDB-4wu3: Structure of the PTP-like myo-inositol phosphatase from Mitsuokel... -

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Basic information

Entry
Database: PDB / ID: 4wu3
TitleStructure of the PTP-like myo-inositol phosphatase from Mitsuokella multacida in complex with myo-inositol-(1,3,4,5)-tetrakisphosphate
ComponentsMYO-INOSITOL PHOSPHOHYDROLASE
KeywordsHYDROLASE
Function / homology
Function and homology information


3-phytase / inositol hexakisphosphate 3-phosphatase activity
Similarity search - Function
Alpha-Beta Plaits - #1690 / Inositol hexakisphosphate / Inositol hexakisphosphate / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain ...Alpha-Beta Plaits - #1690 / Inositol hexakisphosphate / Inositol hexakisphosphate / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / PHOSPHATE ION / Phytase
Similarity search - Component
Biological speciesMitsuokella multacida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBruder, L.M. / Mosimann, S.C.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canada Foundation for Innovation Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Citation
Journal: To Be Published
Title: Structure of the PTP-like phytase from Selenomonas ruminantium in complex with myo-inositol-(1,3,4,5)-tetrakisphosphate
Authors: Bruder, L.M.
#1: Journal: J. Mol. Biol. / Year: 2009
Title: Structural analysis of a multifunctional, tandemly repeated inositol polyphosphatase.
Authors: Gruninger, R.J. / Selinger, L.B. / Mosimann, S.C.
History
DepositionOct 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYO-INOSITOL PHOSPHOHYDROLASE
B: MYO-INOSITOL PHOSPHOHYDROLASE
C: MYO-INOSITOL PHOSPHOHYDROLASE
D: MYO-INOSITOL PHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,46728
Polymers289,7924
Non-polymers4,67524
Water40,7502262
1
A: MYO-INOSITOL PHOSPHOHYDROLASE
B: MYO-INOSITOL PHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,23414
Polymers144,8962
Non-polymers2,33812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-35 kcal/mol
Surface area50300 Å2
MethodPISA
2
C: MYO-INOSITOL PHOSPHOHYDROLASE
D: MYO-INOSITOL PHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,23414
Polymers144,8962
Non-polymers2,33812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-35 kcal/mol
Surface area50320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.899, 86.680, 124.149
Angle α, β, γ (deg.)107.27, 91.69, 90.01
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 47 - 636 / Label seq-ID: 39 - 628

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
MYO-INOSITOL PHOSPHOHYDROLASE


Mass: 72448.023 Da / Num. of mol.: 4 / Fragment: UNP residues 32-640 / Mutation: C250S, C548S
Source method: isolated from a genetically manipulated source
Details: Inactive with C252S/C548S mutations / Source: (gene. exp.) Mitsuokella multacida (bacteria) / Gene: phyA / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3QMF6, 3-phytase
#2: Chemical
ChemComp-4IP / INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE


Mass: 500.075 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H16O18P4
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2262 / 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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 8000, Polyethylene glycol, Tris chloride, beta-mercapto ethanol, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.2→44.54 Å / Num. obs: 146418 / % possible obs: 98.8 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.3 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOLREPphasing
Aimlessdata scaling
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F41

3f41


Resolution: 2.2→44.54 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.052 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21341 2118 1.4 %RANDOM
Rwork0.18979 ---
obs0.19014 144299 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.523 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.13 Å2-0.13 Å2
2---2.05 Å2-0.66 Å2
3---2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19188 0 270 2262 21720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01919980
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218700
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.95927056
X-RAY DIFFRACTIONr_angle_other_deg0.67343116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.51552364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.84924.239972
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.264153484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.83115112
X-RAY DIFFRACTIONr_chiral_restr0.0570.22816
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02122356
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024700
X-RAY DIFFRACTIONr_mcbond_it1.8221.6679456
X-RAY DIFFRACTIONr_mcbond_other1.821.6669455
X-RAY DIFFRACTIONr_mcangle_it2.8042.49211820
Refine LS restraints NCS

Dom-ID: 1 / Number: 5556 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.87

Ens-IDAuth asym-IDRms dev position (Å)
1A3.01
2A1.4
3A3.53
4B3.09
5B2.2
6C3.62
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 151 -
Rwork0.29 10569 -
obs--97.03 %

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