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- PDB-6y88: IGPS (Indole-3-glycerol phosphate synthase) from Pseudomonas aeru... -

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Basic information

Entry
Database: PDB / ID: 6y88
TitleIGPS (Indole-3-glycerol phosphate synthase) from Pseudomonas aeruginosa in complex with substrate inhibitor rCdRP
Components(Indole-3-glycerol phosphate ...) x 2
KeywordsLYASE / Tryptophan biosynthesis / carboxylyase / ba8-barrel / indole synthesis
Function / homology
Function and homology information


indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / L-tryptophan biosynthetic process
Similarity search - Function
Indole-3-glycerol phosphate synthase, conserved site / Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase domain / Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-137 / CITRIC ACID / PHOSPHATE ION / Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09983451737 Å
AuthorsSoderholm, A. / Selmer, M.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2017-03827 Sweden
Knut and Alice Wallenberg FoundationEvolution of new genes and proteins Sweden
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure and kinetics of indole-3-glycerol phosphate synthase from Pseudomonas aeruginosa : Decarboxylation is not essential for indole formation.
Authors: Soderholm, A. / Newton, M.S. / Patrick, W.M. / Selmer, M.
History
DepositionMar 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Indole-3-glycerol phosphate synthase
B: Indole-3-glycerol phosphate synthase
C: Indole-3-glycerol phosphate synthase
D: Indole-3-glycerol phosphate synthase
E: Indole-3-glycerol phosphate synthase
F: Indole-3-glycerol phosphate synthase
G: Indole-3-glycerol phosphate synthase,Indole-3-glycerol phosphate synthase
H: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,50624
Polymers250,1168
Non-polymers3,39016
Water20,3391129
1
A: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9013
Polymers31,4581
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9944
Polymers31,4581
Non-polymers5353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9944
Polymers31,4581
Non-polymers5353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8092
Polymers31,4581
Non-polymers3511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0944
Polymers31,4581
Non-polymers6353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8092
Polymers31,4581
Non-polymers3511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Indole-3-glycerol phosphate synthase,Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0042
Polymers29,9091
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9013
Polymers31,4581
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.705, 150.683, 114.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Indole-3-glycerol phosphate ... , 2 types, 8 molecules ABCDEFHG

#1: Protein
Indole-3-glycerol phosphate synthase / IGPS


Mass: 31458.074 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: trpC, DT376_13060 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A367MAM9, UniProt: P20577*PLUS, indole-3-glycerol-phosphate synthase
#2: Protein Indole-3-glycerol phosphate synthase,Indole-3-glycerol phosphate synthase / IGPS / IGPS


Mass: 29909.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: trpC, DT376_13060 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A367MAM9, UniProt: P20577*PLUS, indole-3-glycerol-phosphate synthase

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Non-polymers , 5 types, 1145 molecules

#3: Chemical
ChemComp-137 / 1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE


Mass: 351.246 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C12H18NO9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1129 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.9 Å3/Da / Density % sol: 56.38 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 3.4
Details: 0.07 M Citric acid, 0.03 M Bis-Tris propane pH 3.4 (Condition G12 from PEG/Ion screen from Hampton Research)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.099→50 Å / Num. obs: 321139 / % possible obs: 100 % / Redundancy: 7.03 % / Biso Wilson estimate: 30.2458918458 Å2 / CC1/2: 0.994 / Net I/σ(I): 7.61
Reflection shellResolution: 2.099→2.23 Å / Mean I/σ(I) obs: 1.73 / Num. unique obs: 51980 / CC1/2: 0.73

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TSM

3tsm


Resolution: 2.09983451737→48.0433596166 Å / SU ML: 0.23247016633 / Cross valid method: FREE R-VALUE / σ(F): 1.1861589204 / Phase error: 21.7744224305
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.218055634217 16096 5.01281544206 %
Rwork0.172852520379 305001 -
obs0.175092930297 321097 99.985676163 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.8851359205 Å2
Refinement stepCycle: LAST / Resolution: 2.09983451737→48.0433596166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16162 0 221 1129 17512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011787944277916651
X-RAY DIFFRACTIONf_angle_d1.0998938078822571
X-RAY DIFFRACTIONf_chiral_restr0.1140743491182702
X-RAY DIFFRACTIONf_plane_restr0.007011092616462994
X-RAY DIFFRACTIONf_dihedral_angle_d17.30334447846334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0999-2.12370.3001827427565380.25772416932910287X-RAY DIFFRACTION99.9630621479
2.1237-2.14870.2970258488225410.24899972329810139X-RAY DIFFRACTION100
2.1487-2.17490.2819726097945310.24032837442110152X-RAY DIFFRACTION99.9812821713
2.1749-2.20240.2837688995785330.23427683632210173X-RAY DIFFRACTION100
2.2024-2.23140.2521437871835360.22213567552610143X-RAY DIFFRACTION99.9719153717
2.2314-2.2620.2860882799795360.23260790035910168X-RAY DIFFRACTION100
2.262-2.29430.275187816155290.22955832692510107X-RAY DIFFRACTION99.9811994736
2.2943-2.32850.2476273584675370.21785741314110207X-RAY DIFFRACTION99.9906933457
2.3285-2.36490.2559212948165410.2149815080910208X-RAY DIFFRACTION100
2.3649-2.40370.2564136701415400.20639384508110120X-RAY DIFFRACTION100
2.4037-2.44510.2389534061635440.19663723826910161X-RAY DIFFRACTION100
2.4451-2.48960.2680109675865350.19749388255910164X-RAY DIFFRACTION100
2.4896-2.53750.2557800796435460.20194493861410230X-RAY DIFFRACTION100
2.5375-2.58930.2560549095655320.1964407877310105X-RAY DIFFRACTION100
2.5893-2.64560.2023590197375350.17129203761110175X-RAY DIFFRACTION100
2.6456-2.70710.2202595775035430.17319370728210172X-RAY DIFFRACTION100
2.7071-2.77480.2437443175875370.17606708864510126X-RAY DIFFRACTION100
2.7748-2.84980.21250041235380.17296692400310181X-RAY DIFFRACTION100
2.8498-2.93360.2364095915595430.17895057651910192X-RAY DIFFRACTION100
2.9336-3.02830.2406262708035300.17636745024310092X-RAY DIFFRACTION100
3.0283-3.13650.2371674844975350.17067778100410218X-RAY DIFFRACTION100
3.1365-3.26210.2304446087175380.17490414833410199X-RAY DIFFRACTION100
3.2621-3.41050.2070301035055330.16237790551310109X-RAY DIFFRACTION100
3.4105-3.59030.1944914443535360.15104516109710222X-RAY DIFFRACTION100
3.5903-3.81510.2095629165155290.14737072352710141X-RAY DIFFRACTION100
3.8151-4.10950.1889999028875390.13973063133110162X-RAY DIFFRACTION100
4.1095-4.52280.1730984119825340.13325881544910153X-RAY DIFFRACTION100
4.5228-5.17660.1482095455665420.1304038786310184X-RAY DIFFRACTION100
5.1766-6.51940.2092191809045370.17160547886710148X-RAY DIFFRACTION100
6.5194-48.04330.201683720625280.18000306212110163X-RAY DIFFRACTION99.682983683

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