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- PDB-6rtz: Light-Regulation of Imidazole Glycerol Phosphate Synthase by Inte... -

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Basic information

Entry
Database: PDB / ID: 6rtz
TitleLight-Regulation of Imidazole Glycerol Phosphate Synthase by Interference with its Allosteric Machinery through Photo-Sensitive Unnatural Amino Acids
Components
  • Imidazole glycerol phosphate synthase subunit HisF
  • Imidazole glycerol phosphate synthase subunit HisH
KeywordsLYASE / unnatural amino acids / phenylalanine-4'-azobenzene (AzoF) / o-nitropiperonyl-O-tyrosine (NPY)
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / glutaminase / glutaminase activity / L-histidine biosynthetic process / lyase activity / cytoplasm
Similarity search - Function
Imidazole glycerol phosphate synthase, subunit H / Histidine biosynthesis, HisF / : / Histidine biosynthesis protein / Histidine biosynthesis protein / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Ribulose-phosphate binding barrel ...Imidazole glycerol phosphate synthase, subunit H / Histidine biosynthesis, HisF / : / Histidine biosynthesis protein / Histidine biosynthesis protein / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Ribulose-phosphate binding barrel / Class I glutamine amidotransferase-like / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Imidazole glycerol phosphate synthase subunit HisF / Imidazole glycerol phosphate synthase subunit HisH
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsKneuttinger, A. / Rajendran, C. / Sterner, R.
CitationJournal: Cell Chem Biol / Year: 2019
Title: Light Regulation of Enzyme Allostery through Photo-responsive Unnatural Amino Acids.
Authors: Kneuttinger, A.C. / Straub, K. / Bittner, P. / Simeth, N.A. / Bruckmann, A. / Busch, F. / Rajendran, C. / Hupfeld, E. / Wysocki, V.H. / Horinek, D. / Konig, B. / Merkl, R. / Sterner, R.
History
DepositionMay 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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: Imidazole glycerol phosphate synthase subunit HisF
B: Imidazole glycerol phosphate synthase subunit HisH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0744
Polymers50,8842
Non-polymers1902
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-22 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.643, 94.643, 166.068
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Imidazole glycerol phosphate synthase subunit HisF / IGP synthase cyclase subunit / IGP synthase subunit HisF / ImGP synthase subunit HisF / IGPS subunit HisF


Mass: 27753.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: hisF, TM_1036 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0C6, imidazole glycerol-phosphate synthase
#2: Protein Imidazole glycerol phosphate synthase subunit HisH / IGP synthase glutaminase subunit / IGP synthase subunit HisH / ImGP synthase subunit HisH / IGPS ...IGP synthase glutaminase subunit / IGP synthase subunit HisH / ImGP synthase subunit HisH / IGPS subunit HisH / TmHisH


Mass: 23130.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: hisH, TM_1038 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0C8, imidazole glycerol-phosphate synthase, glutaminase
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 4.22 Å3/Da / Density % sol: 70.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Apr 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.771→45.87 Å / Num. all: 420130 / Num. obs: 22345 / % possible obs: 98.95 % / Redundancy: 18.8 % / Biso Wilson estimate: 57.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.2061 / Rpim(I) all: 0.04882 / Rrim(I) all: 0.2119 / Net I/σ(I): 4
Reflection shellResolution: 2.771→2.87 Å / Redundancy: 17.9 % / Rmerge(I) obs: 0.9248 / Mean I/σ(I) obs: 2.1 / Num. unique all: 36856 / Num. unique obs: 1996 / CC1/2: 0.853 / Rpim(I) all: 0.2174 / Rrim(I) all: 0.9514 / % possible all: 89.79

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GPW

1gpw


Resolution: 2.87→45.87 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.31
RfactorNum. reflection% reflection
Rfree0.3361 2091 5 %
Rwork0.2742 --
obs0.2773 41792 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.87→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3543 0 10 96 3649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093612
X-RAY DIFFRACTIONf_angle_d1.0764868
X-RAY DIFFRACTIONf_dihedral_angle_d4.0512164
X-RAY DIFFRACTIONf_chiral_restr0.058546
X-RAY DIFFRACTIONf_plane_restr0.006629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.771-2.83550.43871220.39082211X-RAY DIFFRACTION83
2.8355-2.90640.41391400.29522666X-RAY DIFFRACTION100
2.9064-2.98490.32391430.27842697X-RAY DIFFRACTION100
2.9849-3.07280.3431390.2772678X-RAY DIFFRACTION100
3.0728-3.17190.41321370.27372661X-RAY DIFFRACTION100
3.1719-3.28520.32231440.27482682X-RAY DIFFRACTION100
3.2852-3.41670.39441420.27152689X-RAY DIFFRACTION100
3.4167-3.57220.31611360.26822676X-RAY DIFFRACTION100
3.5722-3.76040.31631440.2682678X-RAY DIFFRACTION100
3.7604-3.99590.28921410.24732681X-RAY DIFFRACTION100
3.9959-4.30420.31410.2422675X-RAY DIFFRACTION100
4.3042-4.7370.28441390.24942680X-RAY DIFFRACTION100
4.737-5.42150.31121400.26232663X-RAY DIFFRACTION100
5.4215-6.82690.37641430.28722700X-RAY DIFFRACTION100
6.8269-45.880.38441400.31382664X-RAY DIFFRACTION100

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