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- PDB-7an7: Enzyme of biosynthetic pathway -

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Basic information

Entry
Database: PDB / ID: 7an7
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: 1.81 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)66,03710
Polymers65,0682
Non-polymers9698
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-13 kcal/mol
Surface area22580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.302, 94.778, 71.472
Angle α, β, γ (deg.)90.000, 95.130, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 44 or resid 46...
21(chain B and (resid 3 through 44 or resid 46...

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
11ASNASNLEULEU(chain A and (resid 3 through 44 or resid 46...AA3 - 444 - 45
12GLUGLUPROPRO(chain A and (resid 3 through 44 or resid 46...AA46 - 12847 - 129
13TYRTYRTRPTRP(chain A and (resid 3 through 44 or resid 46...AA130 - 176131 - 177
14GLUGLUGLUGLU(chain A and (resid 3 through 44 or resid 46...AA178 - 284179 - 285
21ASNASNLEULEU(chain B and (resid 3 through 44 or resid 46...BB3 - 444 - 45
22GLUGLUPROPRO(chain B and (resid 3 through 44 or resid 46...BB46 - 12847 - 129
23TYRTYRTRPTRP(chain B and (resid 3 through 44 or resid 46...BB130 - 176131 - 177
24GLUGLUGLUGLU(chain B and (resid 3 through 44 or resid 46...BB178 - 284179 - 285

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Components

#1: Protein Chorismate dehydratase / Menaquinone biosynthetic enzyme MqnA


Mass: 32534.033 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25 % w/v PEG 4000, 100 mM Sodium Citrate, 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-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.81→47.39 Å / Num. obs: 52475 / % possible obs: 97.3 % / Redundancy: 2.742 % / Biso Wilson estimate: 27.739 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.067 / Χ2: 0.995 / Net I/σ(I): 12.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.81-1.921.50.3641.7476760.8230.51488.5
1.92-2.051.6780.2123.4280380.9110.398.2
2.05-2.212.2990.1656.2674330.970.21198
2.21-2.422.7930.1269.8568990.9830.15498.5
2.42-2.713.5530.08913.8363130.9930.10499.7
2.71-3.123.750.0618.8456060.9960.0799.8
3.12-3.823.7240.04226.9947100.9980.04999.6
3.82-5.393.7480.03234.0636820.9980.03799.5

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Phasing

PhasingMethod: molecular replacement

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Processing

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

7ahr


Resolution: 1.81→47.39 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 2623 5 %
Rwork0.1977 49840 -
obs0.1996 52463 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.55 Å2 / Biso mean: 23.6981 Å2 / Biso min: 10.47 Å2
Refinement stepCycle: final / Resolution: 1.81→47.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 81 528 5033
Biso mean--26.43 30.33 -
Num. residues----565
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2637X-RAY DIFFRACTION4.936TORSIONAL
12B2637X-RAY DIFFRACTION4.936TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.81-1.840.35531020.3302191271
1.84-1.870.40031370.3192258397
1.87-1.910.35691370.3297260997
1.91-1.950.38341370.3053259497
1.95-20.29491390.247263998
2-2.050.27221410.2243268599
2.05-2.10.25831360.2133258296
2.1-2.170.21031380.2053264799
2.17-2.240.2571420.2273270099
2.24-2.320.35551390.2489265198
2.32-2.410.25321390.20082644100
2.41-2.520.25071410.1892684100
2.52-2.650.22961420.19232702100
2.65-2.820.24521430.20082686100
2.82-3.040.24751410.19752686100
3.04-3.340.23421410.18562684100
3.34-3.820.18511430.1642700100
3.82-4.820.15141420.1405271299
4.82-100.19111430.1665274099

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