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- PDB-7an5: Enzyme of biosynthetic pathway -

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Basic information

Entry
Database: PDB / ID: 7an5
TitleEnzyme of biosynthetic pathway
ComponentsChorismate dehydratase
KeywordsBIOSYNTHETIC PROTEIN / Enzyme activity / Biosynthetic pathway
Function / homologychorismate dehydratase / Chorismate dehydratase / Menaquinone biosynthesis enzyme / Menaquinone biosynthesis / hydro-lyase activity / menaquinone biosynthetic process / 3-[(1-Carboxyvinyl)oxy]benzoic acid / Chorismate dehydratase
Function and homology information
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 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 / pdbx_initial_refinement_model

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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)65,5384
Polymers65,1222
Non-polymers4162
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-9 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.918, 94.464, 71.692
Angle α, β, γ (deg.)90.000, 95.200, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 163 or resid 165 through 302))
21(chain B and (resid 4 through 163 or resid 165 through 302))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 4 through 163 or resid 165 through 302))A4 - 163
121(chain A and (resid 4 through 163 or resid 165 through 302))A165 - 302
211(chain B and (resid 4 through 163 or resid 165 through 302))B4 - 163
221(chain B and (resid 4 through 163 or resid 165 through 302))B165 - 302

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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 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 / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris HCl 200 mM sodium acetate 30 % PEG 4000

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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: 1.91→43.74 Å / Num. obs: 41744 / % possible obs: 92.1 % / Redundancy: 2.642 % / Biso Wilson estimate: 29.927 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.085 / Χ2: 0.971 / Net I/σ(I): 12.74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.91-2.021.7350.606252750.5530.85772.5
2.02-2.162.0070.334.1459820.790.44987.2
2.16-2.342.3110.2636.6858140.8990.3491
2.34-2.562.7860.1439.6758770.9740.17599.7
2.56-2.863.1920.10412.8853200.990.12599.8
2.86-3.33.190.06717.7747000.9950.0899.7
3.3-4.033.0680.04625.339510.9970.05698.7
4.03-5.683.1760.03530.4230770.9980.04299.4
5.68-103.1250.03331.7317480.9980.04198.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
PHENIX1.17.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AHR

7ahr


Resolution: 1.91→43.737 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 2085 5 %
Rwork0.2015 39589 -
obs0.2032 41674 91.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.7 Å2 / Biso mean: 26.6124 Å2 / Biso min: 11.35 Å2
Refinement stepCycle: final / Resolution: 1.91→43.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4427 0 30 386 4843
Biso mean--22.31 31.47 -
Num. residues----565
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2672X-RAY DIFFRACTION4.153TORSIONAL
12B2672X-RAY DIFFRACTION4.153TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.91-1.950.39711030.3954195169
1.95-20.37081140.3502219376
2-2.050.36431090.3135203672
2.06-2.120.29011340.2418255388
2.12-2.180.27531450.2286274696
2.18-2.260.321260.2598240384
2.26-2.350.29511470.2494278398
2.35-2.460.26581500.21772850100
2.46-2.590.28241510.21172866100
2.59-2.750.24511520.20162888100
2.75-2.960.25881490.20442842100
2.96-3.260.22221510.19872873100
3.26-3.730.18821500.1712285099
3.73-4.70.18111500.1485284799
4.7-100.18211540.1681290899

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