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- PDB-1gr0: myo-inositol 1-phosphate synthase from Mycobacterium tuberculosis... -

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Basic information

Entry
Database: PDB / ID: 1gr0
Titlemyo-inositol 1-phosphate synthase from Mycobacterium tuberculosis in complex with NAD and zinc.
ComponentsINOSITOL-3-PHOSPHATE SYNTHASE
KeywordsISOMERASE / OXIDOREDUCTASE / PSI / PROTEIN STRUCTURE INITIATIVE / TB STRUCTURAL GENOMICS CONSORTIUM / TB / TBSGC
Function / homology
Function and homology information


Mycothiol biosynthesis / inositol-3-phosphate synthase / mycothiol biosynthetic process / inositol-3-phosphate synthase activity / inositol biosynthetic process / phospholipid biosynthetic process / : / zinc ion binding / cytosol
Similarity search - Function
Myo-inositol 1-phosphate synthase, actinobacteria / 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, actinobacteria / 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
CACODYLATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Inositol-3-phosphate synthase / Inositol-3-phosphate synthase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsNorman, R.A. / Murray-Rust, J. / McDonald, N.Q. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Structure / Year: 2002
Title: Crystal Structure of Inositol 1-Phosphate Synthase from Mycobacterium Tuberculosis, a Key Enzyme in Phosphatidylinositol Synthesis
Authors: Norman, R.A. / Mcalister, M.S.B. / Murray-Rust, J. / Movahedzadeh, F. / Stoker, N.G. / Mcdonald, N.Q.
History
DepositionDec 10, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 21, 2016Group: Structure summary
Revision 1.3Aug 21, 2019Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INOSITOL-3-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0054
Polymers40,1391
Non-polymers8663
Water3,063170
1
A: INOSITOL-3-PHOSPHATE SYNTHASE
hetero molecules

A: INOSITOL-3-PHOSPHATE SYNTHASE
hetero molecules

A: INOSITOL-3-PHOSPHATE SYNTHASE
hetero molecules

A: INOSITOL-3-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,02116
Polymers160,5584
Non-polymers3,46312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation2_555-x,-y,z1
Buried area17360 Å2
ΔGint-243.9 kcal/mol
Surface area46660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.195, 116.195, 64.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein INOSITOL-3-PHOSPHATE SYNTHASE / / IPS / MYO-INOSITOL-1-PHOSPHATE SYNTHASE / MI-1-P SYNTHASE / MIP SYNTHASE / HYPOTHETICAL 40.1 KDA ...IPS / MYO-INOSITOL-1-PHOSPHATE SYNTHASE / MI-1-P SYNTHASE / MIP SYNTHASE / HYPOTHETICAL 40.1 KDA PROTEIN RV0046C


Mass: 40139.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P71703, UniProt: P9WKI1*PLUS, inositol-3-phosphate synthase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ENZYME INOSITOL-1-PHOSPHATE SYNTHASE IS PART OF THE PHOSPHATIDYLINOSITOL BIOSYNTHESIS PATHWAY ...THE ENZYME INOSITOL-1-PHOSPHATE SYNTHASE IS PART OF THE PHOSPHATIDYLINOSITOL BIOSYNTHESIS PATHWAY AND CATALYSES THE CONVERSION OF INOSITOL-1-PHOSPHATE FROM GLUCOSE-6-PHOSPHATE.

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 7
Details: OPTIMAL CRYSTALLISATION CONDITIONS: PEG 4000 (6.2-6.7% W/V), SODIUM CACODYLATE (50MM, PH7.0), CALCIUM ACETATE (100MM)., pH 7.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16.2-6.7 %(w/v)PEG40001reservoir
250 mMsodium cacodylate1reservoirpH7.0
3100 mMcalcium acetate1reservoir
40.400 mMNAD1drop
55.0-5.5 %(w/v)PEG40001drop
650 mMsodium cacodylate1droppH7.0
7100 mMcalcium acetate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2000 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→24.79 Å / Num. obs: 29486 / % possible obs: 90 % / Redundancy: 2.7 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 7.7
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.8 / % possible all: 87
Reflection
*PLUS
% possible obs: 89.9 % / Num. measured all: 80189
Reflection shell
*PLUS
% possible obs: 86.6 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTIALLY REFINED MODEL OBTAINED FROM MAD PHASES

Resolution: 1.95→24.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3021712.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE SIDE CHAINS FOR THE FOLLOWING RESIDUES WERE DISORDERED IN ELECTRON DENSITY: THR A 14, ARG A 60, ASP A 268
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1389 4.9 %RANDOM
Rwork0.211 ---
obs0.211 28153 85.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.409 Å2 / ksol: 0.382561 e/Å3
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1--8 Å20 Å20 Å2
2---8 Å20 Å2
3---16.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.95→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 50 170 2726
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.722
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 233 5.4 %
Rwork0.323 4115 -
obs--81.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NAD.PARAMNAD.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION5CAC.PARAMCAC.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.09

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