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- PDB-7nwr: Structure of BT1526, a myo-inositol-1-phosphate synthase -

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Basic information

Entry
Database: PDB / ID: 7nwr
TitleStructure of BT1526, a myo-inositol-1-phosphate synthase
ComponentsInositol-3-phosphate synthase
KeywordsISOMERASE / inositol-1-phosphate / NAD / inositol lipid
Function / homology
Function and homology information


inositol-3-phosphate synthase activity / inositol biosynthetic process / phospholipid biosynthetic process / membrane => GO:0016020
Similarity search - Function
Myo-inositol-1-phosphate synthase / Myo-inositol-1-phosphate synthase / Myo-inositol-1-phosphate synthase, GAPDH-like / Myo-inositol-1-phosphate synthase / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Inositol-3-phosphate synthase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBasle, A. / Tang, G. / Marles-Wright, J. / Campopiano, D.
Funding support2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V001620/1
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V00168X/1
CitationJournal: Nat Microbiol / Year: 2022
Title: Characterization of inositol lipid metabolism in gut-associated Bacteroidetes.
Authors: Heaver, S.L. / Le, H.H. / Tang, P. / Basle, A. / Mirretta Barone, C. / Vu, D.L. / Waters, J.L. / Marles-Wright, J. / Johnson, E.L. / Campopiano, D.J. / Ley, R.E.
History
DepositionMar 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
B: Inositol-3-phosphate synthase
A: Inositol-3-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6005
Polymers101,2502
Non-polymers1,3503
Water5,963331
1
B: Inositol-3-phosphate synthase
A: Inositol-3-phosphate synthase
hetero molecules

B: Inositol-3-phosphate synthase
A: Inositol-3-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,20010
Polymers202,5004
Non-polymers2,7006
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area21900 Å2
ΔGint-157 kcal/mol
Surface area54960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.805, 104.563, 124.318
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-502-

NA

21A-739-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 4 - 429 / Label seq-ID: 24 - 449

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11BA
22AB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Inositol-3-phosphate synthase / / Myo-inositol-1-phosphate synthase


Mass: 50625.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BatF92_28780, DW011_10900, DWY18_07415, DXA83_12175, GAG59_16320, GAN91_05515, GAN99_14790, GAO00_21425, HMPREF2534_03028, SAMN02910322_01983
Production host: Escherichia coli (E. coli) / References: UniProt: A0A139K9L9
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM Sodium Formate 100 mM Bis Tris propane pH 6.5 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→58.85 Å / Num. obs: 59644 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.998 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 13.6 % / Num. unique obs: 4334 / CC1/2: 0.541

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
DIALSdata reduction
xia2data reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QVT

3qvt


Resolution: 2→58.847 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.022 / SU ML: 0.132 / Cross valid method: FREE R-VALUE / ESU R: 0.189 / ESU R Free: 0.163 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2252 2989 5.018 %
Rwork0.183 56578 -
all0.185 --
obs-59567 99.963 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.103 Å2
Baniso -1Baniso -2Baniso -3
1--0.185 Å2-0 Å20 Å2
2--0.145 Å2-0 Å2
3---0.041 Å2
Refinement stepCycle: LAST / Resolution: 2→58.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6738 0 89 331 7158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127000
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.6379502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.395851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99423.353340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.903151219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.071533
X-RAY DIFFRACTIONr_chiral_restr0.0960.2917
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025271
X-RAY DIFFRACTIONr_nbd_refined0.2070.23306
X-RAY DIFFRACTIONr_nbtor_refined0.3120.24764
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2388
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2160.211
X-RAY DIFFRACTIONr_mcbond_it2.5413.2423407
X-RAY DIFFRACTIONr_mcangle_it3.3944.854254
X-RAY DIFFRACTIONr_scbond_it3.6673.5063592
X-RAY DIFFRACTIONr_scangle_it5.0785.1285247
X-RAY DIFFRACTIONr_lrange_it6.16744.43410723
X-RAY DIFFRACTIONr_ncsr_local_group_10.0560.0514246
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.055650.05009
12AX-RAY DIFFRACTIONLocal ncs0.055650.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.3082110.28641150.28743270.7850.78599.97690.277
2.052-2.1080.3122140.27940370.2842540.8120.82999.92950.268
2.108-2.1690.2752130.24639220.24841370.8660.87199.95170.228
2.169-2.2360.32030.2337690.23439730.860.88699.97480.209
2.236-2.3090.3261980.2437020.24439010.8520.89199.97440.215
2.309-2.390.2291730.21336170.21437920.9190.91599.94730.184
2.39-2.480.2761960.21234210.21536190.8930.91299.94470.182
2.48-2.5810.2671630.19233290.19534940.910.93599.94280.163
2.581-2.6960.2291670.18632030.18833710.9380.94299.97030.159
2.696-2.8270.2331630.18330670.18532300.9360.9481000.156
2.827-2.9790.2611530.20128970.20330500.9090.9371000.174
2.979-3.160.2461330.20627890.20829220.9130.931000.183
3.16-3.3770.2731410.19726210.20127630.920.93999.96380.176
3.377-3.6470.2081350.16724200.16925550.950.9661000.154
3.647-3.9930.1821110.15622640.15723750.9650.9721000.144
3.993-4.4620.1741170.13720490.13921660.9720.9771000.129
4.462-5.1470.16990.1218240.12219230.9760.9821000.114
5.147-6.2920.202880.16215510.16516390.9670.9681000.152
6.292-8.8480.14680.14812380.14813060.9770.9811000.142
8.848-58.8470.203430.1657430.1677890.9620.97599.61980.158

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