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- PDB-8s8s: An induced-fit motion of a mobile loop -

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Basic information

Entry
Database: PDB / ID: 8s8s
TitleAn induced-fit motion of a mobile loop
ComponentsImidazole glycerol phosphate synthase subunit HisF
KeywordsSTRUCTURAL PROTEIN / histidine and purine biosynthesis
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
Imidazole glycerol phosphate synthase subunit HisF
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.314 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
A: Imidazole glycerol phosphate synthase subunit HisF


Theoretical massNumber of molelcules
Total (without water)27,6061
Polymers27,6061
Non-polymers00
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10900 Å2
Unit cell
Length a, b, c (Å)44.272, 58.059, 82.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 27605.686 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
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: 1.92 Å3/Da / Density % sol: 35.86 %
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: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.314→47.46 Å / Num. obs: 49373 / % possible obs: 96.16 % / Redundancy: 12.3 % / CC1/2: 0.999 / Net I/σ(I): 12.86
Reflection shellResolution: 1.314→47.46 Å / Num. unique obs: 49373 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.314→47.458 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 1999 4.05 %
Rwork0.188 --
obs0.1889 49361 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.314→47.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 0 258 2181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052043
X-RAY DIFFRACTIONf_angle_d0.762769
X-RAY DIFFRACTIONf_dihedral_angle_d5.7661180
X-RAY DIFFRACTIONf_chiral_restr0.076324
X-RAY DIFFRACTIONf_plane_restr0.004360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.314-1.34660.46371010.44752410X-RAY DIFFRACTION69
1.3466-1.38310.42521260.42092961X-RAY DIFFRACTION85
1.3831-1.42380.35181420.37393350X-RAY DIFFRACTION97
1.4238-1.46970.38041440.30663436X-RAY DIFFRACTION99
1.4697-1.52220.26061470.26893475X-RAY DIFFRACTION100
1.5222-1.58320.25461470.24393476X-RAY DIFFRACTION99
1.5832-1.65530.25551470.18573482X-RAY DIFFRACTION100
1.6553-1.74250.22411460.19243447X-RAY DIFFRACTION99
1.7425-1.85170.22521470.18993494X-RAY DIFFRACTION100
1.8517-1.99470.19641480.18893498X-RAY DIFFRACTION100
1.9947-2.19540.19231490.17683537X-RAY DIFFRACTION100
2.1954-2.51310.19511480.17643499X-RAY DIFFRACTION99
2.5131-3.16610.17971520.17983588X-RAY DIFFRACTION100
3.1661-47.40.19161550.15813709X-RAY DIFFRACTION99

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