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- PDB-7qc3: HisF from T. maritima -

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Basic information

Entry
Database: PDB / ID: 7qc3
TitleHisF from T. maritima
ComponentsImidazole glycerol phosphate synthase subunit HisF
KeywordsMETAL BINDING PROTEIN / BETA BARREL / ARTIFICIAL METALLOENZYME / PROTEIN DESIGN / OXIDOREDUCTASE
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: 1.65 Å
AuthorsBeaumet, M. / Dose, A. / Braeuer, A. / Mahy, J. / Ghattas, W. / Groll, M. / Hess, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme283570European Union
CitationJournal: J.Inorg.Biochem. / Year: 2022
Title: An artificial metalloprotein with metal-adaptive coordination sites and Ni-dependent quercetinase activity.
Authors: Beaumet, M. / Dose, A. / Brauer, A. / Mahy, J.P. / Ghattas, W. / Groll, M. / Hess, C.R.
History
DepositionNov 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)27,7101
Polymers27,7101
Non-polymers00
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.760, 96.760, 154.250
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-614-

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: 27709.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
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.: 359 / 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

Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: 100 mM TRIS, 23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 50620 / % possible obs: 97.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.2
Reflection shellResolution: 1.65→1.75 Å / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8212 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A0N

2a0n


Resolution: 1.65→15 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.718 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.157 2527 5 %RANDOM
Rwork0.1333 ---
obs0.1345 48014 97.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.8 Å2 / Biso mean: 29.013 Å2 / Biso min: 14.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å20 Å2
2--0.15 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: final / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 0 363 2284
Biso mean---45.64 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191948
X-RAY DIFFRACTIONr_bond_other_d0.0020.021908
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.9712627
X-RAY DIFFRACTIONr_angle_other_deg0.92534403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0425248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71224.04884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.14215355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1571514
X-RAY DIFFRACTIONr_chiral_restr0.0840.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022160
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02394
X-RAY DIFFRACTIONr_rigid_bond_restr1.66133855
X-RAY DIFFRACTIONr_sphericity_free28.7045205
X-RAY DIFFRACTIONr_sphericity_bonded10.43153987
LS refinement shellResolution: 1.65→1.692 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 185 -
Rwork0.216 3526 -
all-3711 -
obs--99.78 %

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