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- PDB-8pnj: Chorismate mutase -

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Basic information

Entry
Database: PDB / ID: 8pnj
TitleChorismate mutase
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 II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / 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
DI(HYDROXYETHYL)ETHER / Chem-TSA / chorismate mutase
Similarity search - Component
Biological speciesAequoribacter fuscus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.355 Å
AuthorsKhatanbaatar, T. / Cordara, G. / Krengel, U.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030M_182648 Switzerland
CitationJournal: To Be Published
Title: Structural analysis of chorismate mutase and cyclohexadienyl dehydratase from Pseudomonas aeruginosa
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5508
Polymers47,8541
Non-polymers6967
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-17 kcal/mol
Surface area17550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.608, 105.344, 55.776
Angle α, β, γ (deg.)90.000, 112.484, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein chorismate mutase


Mass: 47854.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequoribacter fuscus (bacteria) / Gene: EYZ66_08225 / Production host: Escherichia coli (E. coli) / Strain (production host): KA29 / References: UniProt: A0A7Z2NRM1

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Non-polymers , 5 types, 48 molecules

#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1:1 volume ratio of 5 mg/ml protein in 20 mM TRIS-HCl, pH=8, 150 uM NaCl buffer and 0.1M BTP, pH=8.5 0.2M KSCN 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.35→46.336 Å / Num. obs: 20939 / % possible obs: 97.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 34.2 Å2 / CC1/2: 0.959 / Net I/σ(I): 4.1
Reflection shellResolution: 2.35→2.44 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1801 / CC1/2: 0.475 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.355→46.336 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.876 / WRfactor Rfree: 0.284 / WRfactor Rwork: 0.215 / SU B: 9.888 / SU ML: 0.228 / Average fsc free: 0.9393 / Average fsc work: 0.9666 / Cross valid method: FREE R-VALUE / ESU R: 0.377 / ESU R Free: 0.283
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2842 979 4.68 %
Rwork0.2148 19940 -
all0.218 --
obs-20919 97.234 %
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: 38.122 Å2
Baniso -1Baniso -2Baniso -3
1--0.155 Å2-0 Å2-0.058 Å2
2--2.847 Å20 Å2
3----1.969 Å2
Refinement stepCycle: LAST / Resolution: 2.355→46.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3087 0 44 41 3172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123422
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163112
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.6444675
X-RAY DIFFRACTIONr_angle_other_deg0.5111.5567286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2065436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.8529.82829
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80410592
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.97410163
X-RAY DIFFRACTIONr_chiral_restr0.0680.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024008
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02668
X-RAY DIFFRACTIONr_nbd_refined0.2260.2707
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.22991
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21640
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21870
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2126
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.4160.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3260.221
X-RAY DIFFRACTIONr_nbd_other0.2730.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2670.27
X-RAY DIFFRACTIONr_mcbond_it2.9753.9021678
X-RAY DIFFRACTIONr_mcbond_other2.973.9021678
X-RAY DIFFRACTIONr_mcangle_it4.4165.8412136
X-RAY DIFFRACTIONr_mcangle_other4.4165.8442137
X-RAY DIFFRACTIONr_scbond_it3.0034.1141744
X-RAY DIFFRACTIONr_scbond_other3.0034.1131745
X-RAY DIFFRACTIONr_scangle_it4.4666.0952539
X-RAY DIFFRACTIONr_scangle_other4.4656.0942540
X-RAY DIFFRACTIONr_lrange_it6.88454.0523770
X-RAY DIFFRACTIONr_lrange_other6.88354.0453770
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
2.355-2.4160.344650.34612560.34615970.9220.91982.71760.346
2.416-2.4820.354800.3113790.31215020.910.93997.13720.31
2.482-2.5540.364890.28814080.29315340.910.95197.5880.288
2.554-2.6320.353580.27313830.27714550.9270.9699.03780.273
2.632-2.7180.289650.20513100.20913960.9460.97498.49570.205
2.718-2.8130.256500.18313130.18613710.9610.9899.41650.183
2.813-2.9190.282630.17412470.17913260.9510.98298.79340.174
2.919-3.0380.264580.18312030.18712680.9580.9899.44790.183
3.038-3.1720.267620.18711460.19112080.9550.981000.187
3.172-3.3260.271430.20211130.20511650.9580.97799.22750.202
3.326-3.5050.318650.24110440.24611230.920.96798.75330.241
3.505-3.7160.301500.2159850.21910460.9420.97498.94840.215
3.716-3.9710.302360.2269380.239900.9330.96698.38380.226
3.971-4.2870.3370.1948690.1989210.9230.97498.37130.194
4.287-4.6920.253380.1667790.178390.9620.98197.37780.166
4.692-5.2390.245350.1957110.1987780.9580.97795.88690.195
5.239-6.0360.259260.2446430.2446840.9480.96697.8070.244
6.036-7.3620.3300.2215360.2265790.9570.97397.75470.221
7.362-10.2820.213140.1784270.1794580.9870.97796.28820.178
10.282-46.3360.159150.2582500.2522720.9860.95997.42650.258

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