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- PDB-8s8r: An induced-fit motion of a mobile loop -

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Basic information

Entry
Database: PDB / ID: 8s8r
TitleAn induced-fit motion of a mobile loop
ComponentsImidazole glycerol phosphate synthase subunit HisF
KeywordsSTRUCTURAL PROTEIN / imidazole glycerol phosphate synthase
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / L-histidine biosynthetic process / lyase activity / cytoplasm
Similarity search - Function
Histidine biosynthesis, HisF / : / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
PHOSPHATE ION / Imidazole glycerol phosphate synthase subunit HisF
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.196 Å
AuthorsRajendran, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Jacs Au / Year: 2024
Title: Conformational Modulation of a Mobile Loop Controls Catalysis in the ( beta alpha ) 8 -Barrel Enzyme of Histidine Biosynthesis HisF.
Authors: Hupfeld, E. / Schlee, S. / Wurm, J.P. / Rajendran, C. / Yehorova, D. / Vos, E. / Ravindra Raju, D. / Kamerlin, S.C.L. / Sprangers, R. / Sterner, R.
History
DepositionMar 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Imidazole glycerol phosphate synthase subunit HisF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8543
Polymers27,6641
Non-polymers1902
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-16 kcal/mol
Surface area11060 Å2
Unit cell
Length a, b, c (Å)79.321, 44.206, 63.460
Angle α, β, γ (deg.)90.00, 111.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-596-

HOH

21D-615-

HOH

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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: 27663.748 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.87 Å3/Da / Density % sol: 34.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: ammonium phosphate

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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 200K / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.19→36.81 Å / Num. obs: 62429 / % possible obs: 96.59 % / Redundancy: 6.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.02606 / Net I/σ(I): 37.69
Reflection shellResolution: 1.196→35.07 Å / Num. unique obs: 62429 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.196→36 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2084 2012 3.23 %
Rwork0.1956 --
obs0.196 62308 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.196→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 10 281 2234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051988
X-RAY DIFFRACTIONf_angle_d0.7842680
X-RAY DIFFRACTIONf_dihedral_angle_d2.5881646
X-RAY DIFFRACTIONf_chiral_restr0.076314
X-RAY DIFFRACTIONf_plane_restr0.005342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.196-1.22590.20361340.21873977X-RAY DIFFRACTION89
1.2259-1.25910.24031310.21544042X-RAY DIFFRACTION92
1.2591-1.29610.23221400.21154126X-RAY DIFFRACTION93
1.2961-1.33790.20911400.2134116X-RAY DIFFRACTION93
1.3379-1.38580.26381340.21584238X-RAY DIFFRACTION95
1.3858-1.44130.2471460.21044246X-RAY DIFFRACTION96
1.4413-1.50690.23011430.19924370X-RAY DIFFRACTION98
1.5069-1.58630.21331440.18964399X-RAY DIFFRACTION99
1.5863-1.68570.21311500.19024395X-RAY DIFFRACTION99
1.6857-1.81580.22081480.19414437X-RAY DIFFRACTION99
1.8158-1.990.19751460.18964426X-RAY DIFFRACTION99
1.9986-2.28770.18391500.18054467X-RAY DIFFRACTION100
2.2877-2.88210.20061550.20564488X-RAY DIFFRACTION100
2.8821-360.20721510.19114569X-RAY DIFFRACTION100

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