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- PDB-7an6: Enzyme of biosynthetic pathway -

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Basic information

Entry
Database: PDB / ID: 7an6
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 A3
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 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
DepositionOct 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)65,5815
Polymers65,0362
Non-polymers5443
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-8 kcal/mol
Surface area23400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.209, 95.199, 72.504
Angle α, β, γ (deg.)90.000, 93.540, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 112 or resid 114...
21(chain B and (resid 1 through 112 or resid 114...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALSERSER(chain A and (resid 1 through 112 or resid 114...AA1 - 1122 - 113
12ARGARGPROPRO(chain A and (resid 1 through 112 or resid 114...AA114 - 163115 - 164
13TYRTYRTYRTYR(chain A and (resid 1 through 112 or resid 114...AA165166
21VALVALSERSER(chain B and (resid 1 through 112 or resid 114...BB1 - 1122 - 113
22ARGARGPROPRO(chain B and (resid 1 through 112 or resid 114...BB114 - 163115 - 164
23TYRTYRTYRTYR(chain B and (resid 1 through 112 or resid 114...BB165166

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Components

#1: Protein Chorismate dehydratase / Menaquinone biosynthetic enzyme MqnA


Mass: 32518.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Gene: mqnA, SCO4506 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L0T8, 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES Sodium salt, 600mM Sodium chloride, 20% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.91→35.892 Å / Num. obs: 45399 / % possible obs: 98.1 % / Redundancy: 2.973 % / Biso Wilson estimate: 29.863 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.124 / Χ2: 1.011 / Net I/σ(I): 9.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.91-2.031.6670.9121.368270.5331.28991.7
2.03-2.172.120.4782.6768500.7610.63798.1
2.17-2.342.6980.3734.3664920.8310.4799.3
2.34-2.563.2470.286.4559710.9280.33799.6
2.56-2.863.7390.29.0954050.9780.23399.5
2.86-3.33.7580.11213.7448080.9910.1399.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AHR

7ahr


Resolution: 1.91→35.89 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 2269 5 %
Rwork0.2101 43130 -
obs0.2118 45399 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.31 Å2 / Biso mean: 23.3287 Å2 / Biso min: 7.11 Å2
Refinement stepCycle: final / Resolution: 1.91→35.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4464 0 38 353 4855
Biso mean--26.59 26.48 -
Num. residues----570
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2691X-RAY DIFFRACTION3.42TORSIONAL
12B2691X-RAY DIFFRACTION3.42TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.91-1.950.38071180.3618224583
1.95-20.37191420.3131268797
2-2.050.34031380.2943262897
2.05-2.10.31241430.2712271398
2.1-2.170.31371420.2697268999
2.17-2.240.28611430.2485272599
2.24-2.320.26491430.2454272299
2.32-2.410.28251430.22972720100
2.41-2.520.30691440.23432729100
2.52-2.650.24171440.22172738100
2.65-2.820.24751440.20922730100
2.82-3.030.24511440.21062739100
3.03-3.340.23361450.19452757100

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