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- PDB-8cq3: Bifunctional chorismate mutase/cyclohexadienyl dehydratase from A... -

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Basic information

Entry
Database: PDB / ID: 8cq3
TitleBifunctional chorismate mutase/cyclohexadienyl dehydratase from Aequoribacter fuscus
Componentschorismate mutase
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 / homology
Function and homology information


chorismate metabolic process / chorismate mutase / chorismate mutase activity
Similarity search - Function
Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF
Similarity search - Domain/homology
ACETATE ION / chorismate mutase
Similarity search - Component
Biological speciesAequoribacter fuscus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 1.2Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0675
Polymers47,8541
Non-polymers2134
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-15 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.419, 98.760, 55.336
Angle α, β, γ (deg.)90.000, 108.519, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein chorismate mutase


Mass: 47854.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ACT: acetate / Source: (gene. exp.) Aequoribacter fuscus (bacteria) / Gene: EYZ66_08225 / Production host: Escherichia coli (E. coli) / Strain (production host): KA29 / References: UniProt: A0A7Z2NRM1
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Bis-TRIS propane, pH=7.5 0.2 M Sodium acetate 20% w/v PEG 3350 5 mg/mL protein in 20 mM TRIS-HCl, pH=8, 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.55→52.5 Å / Num. obs: 33225 / % possible obs: 88.9 % / Redundancy: 6.5 % / CC1/2: 0.997 / Net I/σ(I): 9.3
Reflection shellResolution: 1.55→1.73 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2216 / CC1/2: 0.529 / % possible all: 69.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→52.47 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.001 / SU ML: 0.105 / Cross valid method: FREE R-VALUE / ESU R: 0.153 / ESU R Free: 0.149
RfactorNum. reflection% reflection
Rfree0.2511 1578 4.749 %
Rwork0.1975 31647 -
all0.2 --
obs-33225 61.729 %
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: 24.704 Å2
Baniso -1Baniso -2Baniso -3
1-0.358 Å2-0 Å20.033 Å2
2---0.22 Å2-0 Å2
3----0.131 Å2
Refinement stepCycle: LAST / Resolution: 1.55→52.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3079 0 13 117 3209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123218
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163065
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.6524377
X-RAY DIFFRACTIONr_angle_other_deg0.5181.5757055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3915401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.574523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87310558
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.54810151
X-RAY DIFFRACTIONr_chiral_restr0.0770.2504
X-RAY DIFFRACTIONr_chiral_restr_other0.0440.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023805
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02735
X-RAY DIFFRACTIONr_nbd_refined0.2310.2653
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.22758
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21596
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21818
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2127
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2490.215
X-RAY DIFFRACTIONr_nbd_other0.1630.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2130.26
X-RAY DIFFRACTIONr_mcbond_it2.5092.3581592
X-RAY DIFFRACTIONr_mcbond_other2.5022.3581589
X-RAY DIFFRACTIONr_mcangle_it3.8124.2241995
X-RAY DIFFRACTIONr_mcangle_other3.8114.2281996
X-RAY DIFFRACTIONr_scbond_it3.2152.7761626
X-RAY DIFFRACTIONr_scbond_other3.2142.7761627
X-RAY DIFFRACTIONr_scangle_it5.0584.932382
X-RAY DIFFRACTIONr_scangle_other5.0574.932383
X-RAY DIFFRACTIONr_lrange_it6.62925.0643583
X-RAY DIFFRACTIONr_lrange_other6.6224.9233569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.318100.245151X-RAY DIFFRACTION4.0321
1.59-1.6330.3160.319293X-RAY DIFFRACTION8.026
1.633-1.680.274320.334623X-RAY DIFFRACTION17.462
1.68-1.7320.396530.3121102X-RAY DIFFRACTION31.25
1.732-1.7880.342550.2811360X-RAY DIFFRACTION40.417
1.788-1.8510.282850.2621626X-RAY DIFFRACTION49.8108
1.851-1.9210.364890.2861946X-RAY DIFFRACTION60.9646
1.921-1.9990.3311140.2652231X-RAY DIFFRACTION74.634
1.999-2.0880.3041160.2582539X-RAY DIFFRACTION87.5371
2.088-2.190.3041490.232766X-RAY DIFFRACTION99.2509
2.19-2.3080.3061350.2562651X-RAY DIFFRACTION99.4645
2.308-2.4470.249900.2152530X-RAY DIFFRACTION99.9237
2.447-2.6160.2781340.1942291X-RAY DIFFRACTION98.1384
2.616-2.8250.317520.2031130X-RAY DIFFRACTION51.0583
2.825-3.0940.2561170.1921996X-RAY DIFFRACTION99.9054
3.094-3.4570.229960.1671785X-RAY DIFFRACTION97.7143
3.457-3.9890.185640.1471607X-RAY DIFFRACTION98.121
3.989-4.8790.179830.1331335X-RAY DIFFRACTION100
4.879-6.870.266430.1741098X-RAY DIFFRACTION99.9124
6.87-52.470.167450.163587X-RAY DIFFRACTION99.3711

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