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- PDB-8cq4: Bifunctional cyclohexadienyl dehydratase/chorismate mutase from J... -

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Basic information

Entry
Database: PDB / ID: 8cq4
TitleBifunctional cyclohexadienyl dehydratase/chorismate mutase from Janthinobacterium sp. HH01
ComponentsBifunctional cyclohexadienyl dehydratase/chorismate mutase from Janthinobacterium sp. HH01
KeywordsUNKNOWN FUNCTION / chorismate mutase / cyclohexadienyl dehydratase / chorismate mutase/cyclohexadienyl dehydratase / cyclohexadienyl dehydratase/chorismate mutase / bifunctional chorismate mutase / bifunctional cyclohexadienyl dehydratase / bifunctional enzyme / shikimate pathway enzymes / metabolic enzymes / aromatic amino acid synthesis / protein crystal structure
Biological speciesJanthinobacterium sp. HH01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKhatanbaatar, T. / Cordara, G. / Krengel, U.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030M_182648 Switzerland
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Novel exported fusion enzymes with chorismate mutase and cyclohexadienyl dehydratase activity: Shikimate pathway enzymes teamed up in no man's land.
Authors: Stocker, C. / Khatanbaatar, T. / Bressan, L. / Wurth-Roderer, K. / Cordara, G. / Krengel, U. / Kast, P.
History
DepositionMar 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional cyclohexadienyl dehydratase/chorismate mutase from Janthinobacterium sp. HH01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2472
Polymers47,0521
Non-polymers1951
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint6 kcal/mol
Surface area17770 Å2
Unit cell
Length a, b, c (Å)40.584, 73.985, 131.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bifunctional cyclohexadienyl dehydratase/chorismate mutase from Janthinobacterium sp. HH01


Mass: 47051.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MES: 2-(N-morpholino)ethanesulfonic acid / Source: (gene. exp.) Janthinobacterium sp. HH01 (bacteria) / Gene: ELX09769.1 / Production host: Escherichia coli (E. coli) / Strain (production host): KA29 / References: prephenate dehydratase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% w/v PEG 20 000 20% v/v PEG MME 550 0.03 M Sodium nitrate 0.03 M Disodium hydrogen phosphate 0.03 M Ammonium sulfate 0.1 M MES/imidazole pH 6.5 (Morpheus buffer 1) 3.5 mg/mL protein in 20 mM TRIS-HCl, pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.65→65.6 Å / Num. obs: 35076 / % possible obs: 93 % / Redundancy: 12.7 % / CC1/2: 0.998 / Net I/σ(I): 14.1
Reflection shellResolution: 1.65→1.83 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1754 / CC1/2: 0.542 / % possible all: 54.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→65.6 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.091 / SU ML: 0.101 / Cross valid method: FREE R-VALUE / ESU R: 0.156 / ESU R Free: 0.15
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2453 1717 4.895 %
Rwork0.1917 33359 -
all0.194 --
obs-35076 72.148 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.766 Å2
Baniso -1Baniso -2Baniso -3
1--0.076 Å2-0 Å20 Å2
2--0.113 Å2-0 Å2
3----0.036 Å2
Refinement stepCycle: LAST / Resolution: 1.65→65.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3066 0 12 154 3232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123529
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163416
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.654838
X-RAY DIFFRACTIONr_angle_other_deg0.5451.5757831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3725462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.515544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35910599
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.21210173
X-RAY DIFFRACTIONr_chiral_restr0.0820.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024474
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02902
X-RAY DIFFRACTIONr_nbd_refined0.2220.2782
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.23041
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21713
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21865
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2191
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.4050.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.270.215
X-RAY DIFFRACTIONr_nbd_other0.2150.2100
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.110.26
X-RAY DIFFRACTIONr_mcbond_it2.9162.7821761
X-RAY DIFFRACTIONr_mcbond_other2.912.7811760
X-RAY DIFFRACTIONr_mcangle_it3.8744.9852252
X-RAY DIFFRACTIONr_mcangle_other3.8744.9852253
X-RAY DIFFRACTIONr_scbond_it3.6093.1571768
X-RAY DIFFRACTIONr_scbond_other3.6093.1561766
X-RAY DIFFRACTIONr_scangle_it5.3825.642586
X-RAY DIFFRACTIONr_scangle_other5.3815.642587
X-RAY DIFFRACTIONr_lrange_it6.30628.5454055
X-RAY DIFFRACTIONr_lrange_other6.30628.5464056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.30520.289159X-RAY DIFFRACTION4.5048
1.691-1.7380.348190.315315X-RAY DIFFRACTION9.7804
1.738-1.7880.394190.277509X-RAY DIFFRACTION15.7706
1.788-1.8430.279500.285942X-RAY DIFFRACTION30.0788
1.843-1.9030.288960.2721895X-RAY DIFFRACTION63.1062
1.903-1.970.2761430.2662340X-RAY DIFFRACTION81.5703
1.97-2.0450.3071520.232635X-RAY DIFFRACTION93.5863
2.045-2.1280.2621330.2132732X-RAY DIFFRACTION100
2.128-2.2220.2471360.1962613X-RAY DIFFRACTION100
2.222-2.3310.2461110.1862503X-RAY DIFFRACTION99.9618
2.331-2.4570.2361070.1852401X-RAY DIFFRACTION100
2.457-2.6050.2681140.1842265X-RAY DIFFRACTION100
2.605-2.7850.2411150.1932126X-RAY DIFFRACTION99.9554
2.785-3.0080.235920.1912008X-RAY DIFFRACTION99.9524
3.008-3.2940.2841140.1941816X-RAY DIFFRACTION100
3.294-3.6820.256880.1891699X-RAY DIFFRACTION99.9441
3.682-4.2490.223720.1641483X-RAY DIFFRACTION100
4.249-5.1990.191670.1491288X-RAY DIFFRACTION100
5.199-7.3290.229580.2041010X-RAY DIFFRACTION99.9065
7.329-65.60.222290.21620X-RAY DIFFRACTION100

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