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- PDB-3qw2: L-myo-inositol 1-phosphate synthase from Archaeoglobus mutant N255A -

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Basic information

Entry
Database: PDB / ID: 3qw2
TitleL-myo-inositol 1-phosphate synthase from Archaeoglobus mutant N255A
ComponentsMyo-inositol-1-phosphate synthase (Ino1)
KeywordsISOMERASE / L-myo-inositol 1-phosphate synthase
Function / homology
Function and homology information


inositol-3-phosphate synthase / inositol-3-phosphate synthase activity / inositol biosynthetic process / phospholipid biosynthetic process / nucleotide binding / membrane / cytoplasm
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 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich ...Myo-inositol-1-phosphate synthase / Myo-inositol-1-phosphate synthase / Myo-inositol-1-phosphate synthase, GAPDH-like / Myo-inositol-1-phosphate synthase / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / inositol-3-phosphate synthase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsNeelon, K. / Roberts, M.F. / Stec, B.
CitationJournal: Biophys.J. / Year: 2011
Title: Crystal structure of a trapped catalytic intermediate suggests that forced atomic proximity drives the catalysis of mIPS.
Authors: Neelon, K. / Roberts, M.F. / Stec, B.
History
DepositionFeb 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Dec 7, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: 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
A: Myo-inositol-1-phosphate synthase (Ino1)
B: Myo-inositol-1-phosphate synthase (Ino1)
C: Myo-inositol-1-phosphate synthase (Ino1)
D: Myo-inositol-1-phosphate synthase (Ino1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,00025
Polymers174,8974
Non-polymers4,10421
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23370 Å2
ΔGint-290 kcal/mol
Surface area48560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.512, 88.036, 103.727
Angle α, β, γ (deg.)90.00, 94.91, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 1 - 392 / Label seq-ID: 1 - 392

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Myo-inositol-1-phosphate synthase (Ino1) / mIPS


Mass: 43724.133 Da / Num. of mol.: 4 / Mutation: N255A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF1794, AF_1794 / Production host: Escherichia coli (E. coli) / References: UniProt: O28480, inositol-3-phosphate synthase

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Non-polymers , 6 types, 507 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M calcium chloride, 14% PEG400, 15% PEG1500, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 11, 2005 / Details: Osmic Blue
RadiationMonochromator: Osmic Blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.59→103.14 Å / Num. all: 49303 / Num. obs: 46724 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.174 / Net I/σ(I): 8.5
Reflection shellResolution: 2.59→2.64 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.2 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
CrystalCleardata collection
CrystalCleardata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U1I

1u1i


Resolution: 2.59→103.14 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.862 / SU B: 29.863 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26735 2506 5.1 %RANDOM
Rwork0.18466 ---
obs0.18896 46724 96.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.609 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å2-0.12 Å2
2---1.31 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.59→103.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12324 0 251 486 13061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02212858
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.99217394
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53451564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51324.328536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.235152232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9671548
X-RAY DIFFRACTIONr_chiral_restr0.1070.21888
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219508
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.27286
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.28725
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2768
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2170.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5941.57776
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.091212464
X-RAY DIFFRACTIONr_scbond_it1.45835082
X-RAY DIFFRACTIONr_scangle_it2.3654.54930
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3081 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.440.5
Bmedium positional0.410.5
Cmedium positional0.430.5
Dmedium positional0.520.5
Amedium thermal0.632
Bmedium thermal0.632
Cmedium thermal0.642
Dmedium thermal0.672
LS refinement shellResolution: 2.593→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 182 -
Rwork0.292 3362 -
obs--94.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.32010.5048-0.23091.4888-0.3271.31710.1408-0.17680.02430.2953-0.08150.0089-0.0884-0.0842-0.05930.15950.0090.09990.15880.0060.10160.058614.307750.4452
21.36390.48290.4921.0714-0.11470.28460.1481-0.2255-0.03510.2044-0.09120.12320.0059-0.1234-0.05690.1433-0.00730.00380.17910.00650.161410.228-4.041932.0981
31.11770.69590.90241.3090.55472.1366-0.0554-0.08350.01510.03460.12040.0878-0.0182-0.2208-0.0650.0870.03860.070.17820.0340.1782-7.67249.893634.8005
41.206-0.2954-0.09541.4739-0.35751.4160.12470.317-0.0362-0.4125-0.08230.02690.1081-0.1136-0.04230.1890.023-0.06730.2014-0.04320.09323.0585-9.4342-6.904
50.58330.0465-0.15121.0670.02040.59470.0930.0945-0.028-0.2104-0.09340.0592-0.092-0.11130.00040.13180.03280.00380.1461-0.0110.132113.13756.404413.4057
61.0914-0.38520.80751.85790.89641.70830.07970.0264-0.0779-0.0513-0.07590.21880.0267-0.3191-0.00380.06850.0173-0.0420.29180.03040.201-6.4362-3.6047.0357
70.77970.22780.39420.9927-0.13351.94110.0789-0.0277-0.08090.0716-0.0054-0.02620.2258-0.0147-0.07350.11310.0336-0.03890.0181-0.01540.10836.9555-31.476933.6784
81.0698-0.12640.36610.4622-0.03350.47180.1272-0.1401-0.10410.2315-0.0024-0.0730.0785-0.0066-0.12480.1844-0.0182-0.02220.10360.02390.11429.3249-5.010834.5437
92.0888-0.28850.64041.8773-0.42910.58660.0968-0.0117-0.08420.041-0.0622-0.2313-0.01690.1081-0.03460.06960.0089-0.02650.133-0.01370.155947.4821-17.67529.4125
100.90510.0849-0.33860.8881-0.79912.40340.0442-0.00780.02180.1385-0.0962-0.138-0.21660.01920.05190.0959-0.043-0.00350.02920.00060.088544.566528.326318.0516
111.1128-0.6572-0.22840.5490.41130.73850.15160.11230.1822-0.1834-0.0554-0.199-0.15710.0209-0.09620.17990.01320.04870.09290.01410.148231.92443.452314.724
121.11740.0746-0.90630.90360.00920.8193-0.0496-0.0492-0.04040.0256-0.0609-0.2150.05570.10390.11050.0875-0.0096-0.00450.10980.05350.204151.079812.440523.5208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 227
2X-RAY DIFFRACTION2A228 - 330
3X-RAY DIFFRACTION3A331 - 392
4X-RAY DIFFRACTION4B1 - 227
5X-RAY DIFFRACTION5B228 - 330
6X-RAY DIFFRACTION6B331 - 392
7X-RAY DIFFRACTION7C1 - 227
8X-RAY DIFFRACTION8C228 - 330
9X-RAY DIFFRACTION9C331 - 392
10X-RAY DIFFRACTION10D1 - 227
11X-RAY DIFFRACTION11D228 - 330
12X-RAY DIFFRACTION12D331 - 392

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