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- PDB-3qvs: L-myo-inositol 1-phosphate synthase from Archaeoglobus fulgidus w... -

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Basic information

Entry
Database: PDB / ID: 3qvs
TitleL-myo-inositol 1-phosphate synthase from Archaeoglobus fulgidus wild type
ComponentsMyo-inositol-1-phosphate synthase (Ino1)
KeywordsISOMERASE / NAD binding Rossmann fold / 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: 1.7 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 25, 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 / 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 / _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 / pdbx_initial_refinement_model

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9307
Polymers43,7671
Non-polymers1,1636
Water4,234235
1
A: Myo-inositol-1-phosphate synthase (Ino1)
hetero molecules

A: Myo-inositol-1-phosphate synthase (Ino1)
hetero molecules

A: Myo-inositol-1-phosphate synthase (Ino1)
hetero molecules

A: Myo-inositol-1-phosphate synthase (Ino1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,71928
Polymers175,0694
Non-polymers4,65124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area24070 Å2
ΔGint-233 kcal/mol
Surface area46800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.470, 89.500, 104.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-525-

NA

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 43767.156 Da / Num. of mol.: 1
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, 241 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M calcium chloride, 14% PEG400, 15% PEG1500, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 22, 2004 / 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: 1.69→68.041 Å / Num. all: 42214 / Num. obs: 42024 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 21.1
Reflection shellResolution: 1.69→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2 / Num. unique all: 3897 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U1I

1u1i


Resolution: 1.7→68.04 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.98 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24345 2123 5 %RANDOM
Rwork0.1988 ---
obs0.20104 40084 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.519 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2--2.32 Å20 Å2
3----1.91 Å2
Refine analyzeLuzzati sigma a obs: 0.127 Å
Refinement stepCycle: LAST / Resolution: 1.7→68.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3084 0 74 235 3393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223350
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9944552
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7485425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7524.315146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21415593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7371515
X-RAY DIFFRACTIONr_chiral_restr0.1040.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022506
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21653
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22277
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2224
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.2113
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8071.52001
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.30323232
X-RAY DIFFRACTIONr_scbond_it2.39431394
X-RAY DIFFRACTIONr_scangle_it3.4654.51303
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 161 -
Rwork0.364 2846 -
obs--94.95 %
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)
10.8660.1516-0.00310.4029-0.14110.70260.0736-0.0103-0.0351-0.054-0.02460.04560.15810.0968-0.0490.02320.0451-0.008-0.04920.0008-0.010917.96517.94539.6819
20.0867-0.04540.17230.2468-0.15191.10030.0073-0.0679-0.06340.0521-0.00460.0399-0.01560.0214-0.00270.00410.0291-0.00730.01170.0081-0.041418.507222.382427.4973
30.0598-0.0115-0.08330.1957-0.16710.28940.0542-0.00470.02110.0462-0.05520.05-0.02360.14350.00090.0233-0.0002-0.0155-0.03040.00280.011521.285838.013915.5768
40.97710.6725-0.91612.8637-1.9031.5333-0.0572-0.02830.03530.2230.15060.0056-0.1611-0.0555-0.0934-0.01810.0261-0.01970.0443-0.0108-0.060610.804339.373619.5425
50.0504-0.03710.03010.0631-0.14170.41780.03380.0057-0.00020.0113-0.05870.0336-0.010.1180.02490.01490.0017-0.0047-0.04130.00310.02319.01638.58868.8993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 75
2X-RAY DIFFRACTION2A76 - 188
3X-RAY DIFFRACTION3A189 - 258
4X-RAY DIFFRACTION4A259 - 286
5X-RAY DIFFRACTION5A287 - 392

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