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- PDB-7qc6: HisF_C9A_L50H_I52H mutant (apo) from T. maritima -

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Basic information

Entry
Database: PDB / ID: 7qc6
TitleHisF_C9A_L50H_I52H mutant (apo) 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Imidazole glycerol phosphate synthase subunit HisF
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,8822
Polymers27,7281
Non-polymers1541
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-1 kcal/mol
Surface area11210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.180, 96.180, 153.760
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-543-

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: 27727.666 Da / Num. of mol.: 1 / Mutation: C9A, L50H, I52H
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: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.7 Å3/Da / Density % sol: 66.78 %
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: 0.9779 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 24601 / % possible obs: 97.5 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.3
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 3170

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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: 7QC3

7qc3


Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.6 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.263 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 1225 5 %RANDOM
Rwork0.178 ---
obs0.18 23285 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.54 Å2 / Biso mean: 42.791 Å2 / Biso min: 13.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 8 153 2091
Biso mean--39.8 48.04 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191966
X-RAY DIFFRACTIONr_bond_other_d0.0010.021910
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.9672650
X-RAY DIFFRACTIONr_angle_other_deg0.85534409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9945249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88723.95386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.31215353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7451514
X-RAY DIFFRACTIONr_chiral_restr0.0610.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022179
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02399
X-RAY DIFFRACTIONr_rigid_bond_restr0.96233875
X-RAY DIFFRACTIONr_sphericity_free19.947590
X-RAY DIFFRACTIONr_sphericity_bonded14.68153911
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 88 -
Rwork0.21 1678 -
all-1766 -
obs--98.99 %
Refinement TLS params.Method: refined / Origin x: 17.0769 Å / Origin y: -20.2029 Å / Origin z: 11.0376 Å
111213212223313233
T0.0201 Å20.0076 Å2-0.0026 Å2-0.0128 Å2-0.0026 Å2--0.0062 Å2
L0.1101 °2-0.0413 °2-0.0272 °2-0.2548 °20.0079 °2--0.0546 °2
S-0.0174 Å °-0.0259 Å °-0.0032 Å °0.0101 Å °0.0057 Å °0.0278 Å °0.0037 Å °-0.0005 Å °0.0117 Å °

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