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- PDB-7ywc: Enzyme of biosynthetic pathway -

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Basic information

Entry
Database: PDB / ID: 7ywc
TitleEnzyme of biosynthetic pathway
ComponentsChorismate dehydratase
KeywordsBIOSYNTHETIC PROTEIN / Enzyme activity / Biosynthetic pathway
Function / homologychorismate dehydratase / Chorismate dehydratase / Menaquinone biosynthesis enzyme / Menaquinone biosynthesis / menaquinone biosynthetic process / hydro-lyase activity / Chem-ISJ / Chorismate dehydratase
Function and homology information
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.917 Å
AuthorsArchna, A. / Breithaupt, C. / Stubbs, M.T.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Regional Development Fund Germany
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Mechanism of chorismate dehydratase MqnA, the first enzyme of the futalosine pathway, proceeds via substrate-assisted catalysis.
Authors: Prasad, A. / Breithaupt, C. / Nguyen, D.A. / Lilie, H. / Ziegler, J. / Stubbs, M.T.
History
DepositionFeb 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chorismate dehydratase
B: Chorismate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0379
Polymers65,1242
Non-polymers9137
Water5,278293
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)44.348, 94.819, 72.675
Angle α, β, γ (deg.)90.000, 94.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chorismate dehydratase / Menaquinone biosynthetic enzyme MqnA


Mass: 32562.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: mqnA, HCU77_22945 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6M9XSH4, chorismate dehydratase
#2: Chemical ChemComp-ISJ / (3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1,5-diene-1-carboxylic acid / Chorismic Acid


Mass: 226.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 100 mM Sodiun citrate, 20 % PEG 4000, 200 mM Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 21, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40.088 Å / Num. obs: 43882 / % possible obs: 95.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 28.62 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.01-2.131.760.5462.110134644257580.6740.75689.4
2.13-2.282.2440.2713.9513025604258040.9010.35396.1
2.28-2.462.4870.1985.5613889566555850.9480.25398.6
2.46-2.693.030.1548.0115594518251470.9770.18899.3
2.69-3.013.1360.09511.9414775472447120.990.11599.7
3.01-3.473.150.05120.3312997416541260.9970.06199.1
3.47-4.243.1590.03131.6710989352534790.9990.03898.7
4.24-5.963.1830.02437.458612275627060.9990.02998.2
5.96-40.093.1310.02241.154753158215180.9990.02796

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: None

Resolution: 1.917→40.088 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 2194 5 %
Rwork0.1833 41667 -
obs0.1863 43861 95.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.83 Å2 / Biso mean: 33.2802 Å2 / Biso min: 14.78 Å2
Refinement stepCycle: final / Resolution: 1.917→40.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4466 0 52 293 4811
Biso mean--43.28 38.81 -
Num. residues----569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074642
X-RAY DIFFRACTIONf_angle_d1.1136323
X-RAY DIFFRACTIONf_chiral_restr0.044719
X-RAY DIFFRACTIONf_plane_restr0.006822
X-RAY DIFFRACTIONf_dihedral_angle_d13.9571708
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.917-1.95870.37591110.3452211178
1.9587-2.00420.36151240.3102235587
2.0042-2.05430.33491300.2799246390
2.0543-2.10990.30611330.2563253293
2.1099-2.1720.32281350.2377256595
2.172-2.24210.28931380.2257262596
2.2421-2.32220.28921400.22265497
2.3222-2.41520.27341400.2061267398
2.4152-2.52510.27961420.1994269299
2.5251-2.65820.27511430.1928272499
2.6582-2.82470.2571450.19232738100
2.8247-3.04270.26431420.18192705100
3.0427-3.34870.23041430.172271199
3.3487-3.8330.19981420.1526270999
3.833-4.82790.18211430.1299272299
4.8279-400.20641430.1635268896
Refinement TLS params.Method: refined / Origin x: 9.3387 Å / Origin y: 0.5407 Å / Origin z: 17.9357 Å
111213212223313233
T0.152 Å2-0.0138 Å2-0.0215 Å2-0.2079 Å20.0189 Å2--0.169 Å2
L0.4456 °2-0.6424 °2-0.3752 °2-1.6518 °20.7166 °2--0.634 °2
S-0.0051 Å °0.0092 Å °-0.0074 Å °0.0483 Å °-0.041 Å °-0.0366 Å °0.0356 Å °-0.0282 Å °0.0398 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 286
2X-RAY DIFFRACTION1allA302 - 329
3X-RAY DIFFRACTION1allB2 - 285
4X-RAY DIFFRACTION1allB303 - 330
5X-RAY DIFFRACTION1allS1 - 383
6X-RAY DIFFRACTION1allC1 - 6

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