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- PDB-7qc8: HisF-C9A-D11E-V33A_L50H_I52H mutant in complex with Zn(II) from T... -

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Basic information

Entry
Database: PDB / ID: 7qc8
TitleHisF-C9A-D11E-V33A_L50H_I52H mutant in complex with Zn(II) 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: 1.8 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)27,8753
Polymers27,7141
Non-polymers1612
Water6,197344
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.680, 96.680, 154.420
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-562-

HOH

21A-700-

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: 27713.639 Da / Num. of mol.: 1 / Mutation: C9A, D11E, V33A, 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.76 Å3/Da
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 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 39147 / % possible obs: 97.4 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 25.3
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 5862 / % possible all: 99.4

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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: 1.8→15 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.381 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1592 1953 5 %RANDOM
Rwork0.1382 ---
obs0.1393 37106 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.79 Å2 / Biso mean: 28.698 Å2 / Biso min: 12.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.25 Å2-0 Å2
2--0.49 Å2-0 Å2
3----1.59 Å2
Refinement stepCycle: final / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1929 0 6 348 2283
Biso mean--40.84 41.15 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191962
X-RAY DIFFRACTIONr_bond_other_d0.0020.021901
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9662646
X-RAY DIFFRACTIONr_angle_other_deg0.88734388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1055249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21723.95386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.13215353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8921514
X-RAY DIFFRACTIONr_chiral_restr0.0750.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022179
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02399
X-RAY DIFFRACTIONr_rigid_bond_restr1.49733862
X-RAY DIFFRACTIONr_sphericity_free19.3655198
X-RAY DIFFRACTIONr_sphericity_bonded10.75253986
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 142 -
Rwork0.24 2700 -
all-2842 -
obs--99.47 %
Refinement TLS params.Method: refined / Origin x: 17.1664 Å / Origin y: -20.2697 Å / Origin z: 11.3449 Å
111213212223313233
T0.0049 Å20.0015 Å2-0.0016 Å2-0.0008 Å20.0001 Å2--0.0086 Å2
L0.0593 °2-0.0825 °2-0.0097 °2-0.1639 °20.0043 °2--0.0668 °2
S-0.0078 Å °-0.006 Å °-0.0065 Å °0.0116 Å °0.0067 Å °0.017 Å °0.0117 Å °0.0028 Å °0.0011 Å °

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