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- PDB-6ru0: Light-Regulation of Imidazole Glycerol Phosphate Synthase by Inte... -

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Basic information

Entry
Database: PDB / ID: 6ru0
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 / histidine biosynthetic process / glutaminase activity / glutamine metabolic process / lyase activity / cytoplasm
Similarity search - Function
Imidazole glycerol phosphate synthase, subunit H / Histidine biosynthesis, HisF / Histidine biosynthesis protein / Histidine biosynthesis protein / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Ribulose-phosphate binding barrel / Class I glutamine amidotransferase-like ...Imidazole glycerol phosphate synthase, subunit H / Histidine biosynthesis, HisF / Histidine biosynthesis protein / Histidine biosynthesis protein / Glutamine amidotransferase class-I / Glutamine amidotransferase / 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: 2.648 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Imidazole glycerol phosphate synthase subunit HisF
B: Imidazole glycerol phosphate synthase subunit HisH
C: Imidazole glycerol phosphate synthase subunit HisF
D: Imidazole glycerol phosphate synthase subunit HisH
E: Imidazole glycerol phosphate synthase subunit HisF
F: Imidazole glycerol phosphate synthase subunit HisH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,1199
Polymers152,8346
Non-polymers2853
Water1,08160
1
A: Imidazole glycerol phosphate synthase subunit HisF
B: Imidazole glycerol phosphate synthase subunit HisH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0403
Polymers50,9452
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-13 kcal/mol
Surface area18500 Å2
MethodPISA
2
C: Imidazole glycerol phosphate synthase subunit HisF
D: Imidazole glycerol phosphate synthase subunit HisH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0403
Polymers50,9452
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-15 kcal/mol
Surface area18640 Å2
MethodPISA
3
E: Imidazole glycerol phosphate synthase subunit HisF
F: Imidazole glycerol phosphate synthase subunit HisH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0403
Polymers50,9452
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-15 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.415, 95.415, 165.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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: 27813.967 Da / Num. of mol.: 3
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.: 3
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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.85 Å3/Da / Density % sol: 56.89 %
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: 2.648→45.96 Å / Num. obs: 49035 / % possible obs: 99.74 % / Redundancy: 10.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1046 / Rpim(I) all: 0.03405 / Rrim(I) all: 0.11 / Net I/σ(I): 17.15
Reflection shellResolution: 2.648→2.743 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.782 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4795 / CC1/2: 0.378 / Rpim(I) all: 0.5977 / Rrim(I) all: 1.881 / % possible all: 98.06

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.648→45.964 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2721 4897 5 %
Rwork0.2071 --
obs0.2104 49035 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.648→45.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10648 0 15 60 10723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910879
X-RAY DIFFRACTIONf_angle_d1.15214661
X-RAY DIFFRACTIONf_dihedral_angle_d4.1267829
X-RAY DIFFRACTIONf_chiral_restr0.0631642
X-RAY DIFFRACTIONf_plane_restr0.0061897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6482-2.67830.40781430.34432703X-RAY DIFFRACTION91
2.6783-2.70980.37221680.35753195X-RAY DIFFRACTION100
2.7098-2.74290.36861640.33943116X-RAY DIFFRACTION100
2.7429-2.77760.39851630.33193099X-RAY DIFFRACTION100
2.7776-2.81410.3991660.31533150X-RAY DIFFRACTION100
2.8141-2.85270.38071660.30993153X-RAY DIFFRACTION100
2.8527-2.89340.35641630.30273131X-RAY DIFFRACTION100
2.8934-2.93660.34281620.28583071X-RAY DIFFRACTION100
2.9366-2.98250.35211640.28373111X-RAY DIFFRACTION100
2.9825-3.03140.33561600.27493034X-RAY DIFFRACTION100
3.0314-3.08360.34751680.26573226X-RAY DIFFRACTION100
3.0836-3.13970.37171600.26433026X-RAY DIFFRACTION100
3.1397-3.20010.32221660.25493158X-RAY DIFFRACTION100
3.2001-3.26540.32821620.24433063X-RAY DIFFRACTION100
3.2654-3.33630.33681600.24063058X-RAY DIFFRACTION100
3.3363-3.41390.31491700.24083268X-RAY DIFFRACTION100
3.4139-3.49930.30771620.23953061X-RAY DIFFRACTION100
3.4993-3.59390.3171640.23893122X-RAY DIFFRACTION100
3.5939-3.69960.36371620.26993046X-RAY DIFFRACTION99
3.6996-3.81890.30451680.22573205X-RAY DIFFRACTION99
3.8189-3.95530.26131600.18833040X-RAY DIFFRACTION100
3.9553-4.11360.22911620.18443084X-RAY DIFFRACTION100
4.1136-4.30070.24721660.17253122X-RAY DIFFRACTION100
4.3007-4.52730.22331640.16723128X-RAY DIFFRACTION100
4.5273-4.81060.20771640.16353094X-RAY DIFFRACTION100
4.8106-5.18160.23821640.16293117X-RAY DIFFRACTION100
5.1816-5.70220.24441660.16613149X-RAY DIFFRACTION100
5.7022-6.52530.22691600.19053049X-RAY DIFFRACTION100
6.5253-8.21350.24931660.18653130X-RAY DIFFRACTION100
8.2135-45.97050.22221640.16933114X-RAY DIFFRACTION99

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