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- PDB-8pnh: Chorismate mutase -

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Basic information

Entry
Database: PDB / ID: 8pnh
TitleChorismate mutase
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
Function / homology3-PHENYLPYRUVIC ACID / Chem-TSA
Function and homology information
Biological speciesJanthinobacterium sp. HH01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKhatanbaatar, T. / Cordara, G. / Krengel, U.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030M_182648 Switzerland
CitationJournal: To Be Published
Title: Chorismate mutase
Authors: Khatanbaatar, T. / Cordara, G. / Krengel, U.
History
DepositionJun 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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)47,5404
Polymers47,0521
Non-polymers4883
Water79344
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)41.511, 74.282, 129.352
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
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-TSA / 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID


Mass: 228.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PPY / 3-PHENYLPYRUVIC ACID


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3.5 mg/mL protein in 20 mM TRIS-HCl, pH 8 storage buffer and crystallization solution containing 0.07 M NPS (0.023 M solidum nitrate, 0.023 M disodium hydrogen phosphate and 0.023 M ammonium ...Details: 3.5 mg/mL protein in 20 mM TRIS-HCl, pH 8 storage buffer and crystallization solution containing 0.07 M NPS (0.023 M solidum nitrate, 0.023 M disodium hydrogen phosphate and 0.023 M ammonium sulfate) 9% v/w PEG20K 19% v/w 500MME 0.01 M Imidazole 0.008 M phenylpyruvate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→41.51 Å / Num. obs: 31515 / % possible obs: 97.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 36.6 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1955 / CC1/2: 0.364 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
autoPROCdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→37.318 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.267 / WRfactor Rwork: 0.213 / SU B: 4.542 / SU ML: 0.129 / Average fsc free: 0.9439 / Average fsc work: 0.9645 / Cross valid method: FREE R-VALUE / ESU R: 0.182 / ESU R Free: 0.172
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2667 1623 5.158 %
Rwork0.2127 29845 -
all0.215 --
obs-31468 97.18 %
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: 41.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.439 Å2-0 Å20 Å2
2--0.212 Å2-0 Å2
3----0.651 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 33 44 3071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123285
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163037
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.6474499
X-RAY DIFFRACTIONr_angle_other_deg0.4681.5547075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2635425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.0279.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68710550
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg5.7102
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.09210153
X-RAY DIFFRACTIONr_chiral_restr0.0690.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023939
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02665
X-RAY DIFFRACTIONr_nbd_refined0.220.2691
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.22794
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21621
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21742
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0390.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.214
X-RAY DIFFRACTIONr_nbd_other0.1730.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.28
X-RAY DIFFRACTIONr_mcbond_it3.4384.0761642
X-RAY DIFFRACTIONr_mcbond_other3.4324.0751642
X-RAY DIFFRACTIONr_mcangle_it4.5796.1032086
X-RAY DIFFRACTIONr_mcangle_other4.5816.1042087
X-RAY DIFFRACTIONr_scbond_it4.1384.5561643
X-RAY DIFFRACTIONr_scbond_other4.1424.5631640
X-RAY DIFFRACTIONr_scangle_it6.1146.6642413
X-RAY DIFFRACTIONr_scangle_other6.126.6762408
X-RAY DIFFRACTIONr_lrange_it7.79357.663643
X-RAY DIFFRACTIONr_lrange_other7.79757.6673643
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.9-1.9490.3651080.33621280.33723380.880.91195.63730.336
1.949-2.0020.3661150.29721440.30122980.90.93698.30290.297
2.002-2.060.3411150.24220960.24722440.920.95998.52940.242
2.06-2.1240.2831070.22119870.22421450.9460.96797.62240.221
2.124-2.1930.2351060.22419820.22421330.9610.96697.89030.224
2.193-2.270.2731220.20718100.21120090.9490.97196.16730.207
2.27-2.3550.2881030.21118170.21519550.9520.97198.20970.211
2.355-2.4510.262930.19417840.19819210.9520.97697.70950.194
2.451-2.5590.268770.2116850.21318180.9560.97196.91970.21
2.559-2.6840.2491000.20315790.20617360.9610.97396.71660.203
2.684-2.8280.248790.19615580.19816750.9640.97597.73130.196
2.828-2.9980.314690.20714900.21215900.9280.97398.05030.207
2.998-3.2040.248730.19913900.20114930.9650.97697.99060.199
3.204-3.4580.289680.19312790.19714040.9460.97695.94020.193
3.458-3.7850.238720.19111810.19413000.970.97996.38460.191
3.785-4.2270.253580.19710630.211740.9670.97795.48550.197
4.227-4.870.22580.1959470.19610500.9720.97795.71430.195
4.87-5.9390.316430.2448430.2479180.9350.97196.51420.244
5.939-8.2950.246440.2336600.2347240.9670.97397.23760.233
8.295-37.3180.387130.2514220.2554520.950.95796.23890.251

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