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- PDB-7ahr: Enzyme of biosynthetic pathway -

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Basic information

Entry
Database: PDB / ID: 7ahr
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 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 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
DepositionSep 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: 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)65,6315
Polymers65,1222
Non-polymers5083
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-7 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.341, 87.257, 95.493
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 86 or resid 88 through 286))
21(chain B and (resid 1 through 86 or resid 88 through 107 or resid 110 through 286))

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 86 or resid 88 through 286))AA1 - 862 - 87
12VALVALHISHIS(chain A and (resid 1 through 86 or resid 88 through 286))AA88 - 28689 - 287
21VALVALSERSER(chain B and (resid 1 through 86 or resid 88 through 107 or resid 110 through 286))BB1 - 862 - 87
22VALVALSERSER(chain B and (resid 1 through 86 or resid 88 through 107 or resid 110 through 286))BB88 - 10789 - 108
23ARGARGHISHIS(chain B and (resid 1 through 86 or resid 88 through 107 or resid 110 through 286))BB110 - 286111 - 287

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Components

#1: Protein Chorismate dehydratase / Menaquinone biosynthetic enzyme MqnA


Mass: 32561.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: mqnA, SCO4506 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L0T8, chorismate dehydratase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 4000 and 30% Ethylene glycol

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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 7, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→43.629 Å / Num. obs: 31045 / % possible obs: 98.9 % / Redundancy: 6.115 % / Biso Wilson estimate: 33.081 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.305 / Rrim(I) all: 0.333 / Χ2: 0.93 / Net I/σ(I): 4.98 / Num. measured all: 189855
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.21-2.345.7981.411.4148590.6291.54897.5
2.34-2.56.1691.1661.7446620.7551.27499.2
2.5-2.76.2010.8742.1843440.8670.95498.9
2.7-2.966.2350.5752.9940190.9330.62799.4
2.96-3.316.250.3274.7336610.9760.35699.5
3.31-3.826.2070.1828.5932800.9890.19899.8
3.82-4.676.1810.12411.4227260.9950.13598.2
4.67-6.566.120.13710.2721970.9940.1599.3
6.56-105.7020.08714.5412970.9970.09698.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XDSdata processing
PHASERphasing
PDB_EXTRACT3.25data extraction
Cootmodel building
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NXO

2nxo


Resolution: 2.21→41.89 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2924 1545 4.98 %
Rwork0.2446 29452 -
obs0.247 30997 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.7 Å2 / Biso mean: 29.6473 Å2 / Biso min: 11.58 Å2
Refinement stepCycle: final / Resolution: 2.21→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4487 0 36 200 4723
Biso mean--29.56 27.81 -
Num. residues----571
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2706X-RAY DIFFRACTION5.352TORSIONAL
12B2706X-RAY DIFFRACTION5.352TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.280.43041350.38072547268295
2.28-2.360.35141400.31792636277699
2.36-2.460.36031370.29232618275599
2.46-2.570.33161390.28562661280099
2.57-2.70.32461390.27672659279899
2.7-2.870.34541410.27022667280899
2.87-3.10.32091410.2632688282999
3.1-3.410.25641390.231926852824100
3.41-3.90.26241430.222327292872100
3.9-4.910.26191400.19092716285699
4.91-41.890.22921510.19772846299799

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