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- PDB-7an9: Enzyme of biosynthetic pathway -

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Basic information

Entry
Database: PDB / ID: 7an9
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 / 3-[(1-Carboxyvinyl)oxy]benzoic acid / Chorismate dehydratase
Function and homology information
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.11 Å
AuthorsArchna, A. / Breithaupt, C. / Stubbs, M.T.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Regional Development FundEuropean Union
Citation
Journal: 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.
#1: Journal: Chemrxiv / Year: 2022
Title: Mechanism of the chorismate dehydratase MqnA, first enzyme of the futalosine pathway
Authors: Archna, 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 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 1.3Oct 22, 2025Group: Author supporting evidence / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_audit_support / pdbx_entry_details
Item: _pdbx_audit_support.country / _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 dehydratase
B: Chorismate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5064
Polymers65,0902
Non-polymers4162
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-7 kcal/mol
Surface area22400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.905, 94.149, 73.237
Angle α, β, γ (deg.)90.000, 93.510, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 283 or resid 302))
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 6 through 283 or resid 302))A0
211chain BB6 - 302

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Components

#1: Protein Chorismate dehydratase / Menaquinone biosynthetic enzyme MqnA


Mass: 32545.057 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-RDH / 3-[(1-Carboxyvinyl)oxy]benzoic acid / 3-(3-oxidanyl-3-oxidanylidene-prop-1-en-2-yl)oxybenzoic acid


Mass: 208.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 % w/v PEG 4000, 100 mM MES Sodium Salt, 200 mM Magnesium Chloride

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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: Dec 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.11→47.074 Å / Num. obs: 59519 / % possible obs: 90.8 % / Redundancy: 1.752 % / Biso Wilson estimate: 32.695 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.128 / Χ2: 1.003 / Net I/σ(I): 6.53 / Num. measured all: 104278
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.11-2.241.5610.4471.3977920.8240.6173.3
2.24-2.41.6150.3662.0582320.8480.49783.4
2.4-2.591.7330.3052.885890.880.41392.5
2.59-2.831.8230.2313.9683530.9240.31597.6
2.83-3.171.8250.1395.8875500.9670.1998.3
3.17-3.651.8330.0789.7266900.9840.10798.3
3.65-4.471.830.04614.4456280.9930.06498
4.47-6.291.8490.0415.8943530.9960.05597.4
6.29-101.8480.03518.8923320.9960.04994

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Phasing

PhasingMethod: molecular replacement

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Processing

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

7ahr


Resolution: 2.11→47.07 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 1649 5.01 %
Rwork0.2097 31283 -
obs0.2121 32932 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.59 Å2 / Biso mean: 29.983 Å2 / Biso min: 13.82 Å2
Refinement stepCycle: final / Resolution: 2.11→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 0 30 213 4613
Biso mean--21.93 32 -
Num. residues----558
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2661X-RAY DIFFRACTION6.686TORSIONAL
12B2661X-RAY DIFFRACTION6.686TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.11-2.180.2891260.2972238590
2.18-2.250.36211380.2757260099
2.25-2.330.32991360.27182592100
2.33-2.420.29281390.26042641100
2.42-2.530.30291380.25122629100
2.53-2.660.30361390.23772619100
2.66-2.830.27331370.22432619100
2.83-3.050.26381400.21742640100
3.05-3.350.24321380.20412628100
3.36-3.840.22311380.18262621100
3.84-4.840.21361400.1622658100
4.84-100.22981400.1868265199

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