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- PDB-6lk2: Crystal structure of Providencia alcalifaciens 3-dehydroquinate s... -

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Basic information

Entry
Database: PDB / ID: 6lk2
TitleCrystal structure of Providencia alcalifaciens 3-dehydroquinate synthase (DHQS) in complex with Mg2+, NAD and chlorogenic acid
Components3-dehydroquinate synthase
KeywordsLYASE / Rossmann fold / Cytoplasm / Metal-binding / NAD-binding / chlorogenic acid
Function / homology
Function and homology information


3-dehydroquinate synthase / 3-dehydroquinate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
3-dehydroquinate synthase family / 3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase N-terminal
Similarity search - Domain/homology
Chem-7LH / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / 3-dehydroquinate synthase
Similarity search - Component
Biological speciesProvidencia alcalifaciens F90-2004 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsNeetu, N. / Katiki, M. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB) India
Citation
Journal: J.Bacteriol. / Year: 2020
Title: Structural and Biochemical Analyses Reveal that Chlorogenic Acid Inhibits the Shikimate Pathway.
Authors: Neetu, N. / Katiki, M. / Dev, A. / Gaur, S. / Tomar, S. / Kumar, P.
#1: Journal: To Be Published
Title: Crystal structure of Providencia alcalifaciens 3-dehydroquinate synthase (DHQS) in complex with Mg2+ and NAD
Authors: Neetu, N. / Katiki, M. / Kumar, P.
History
DepositionDec 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: 3-dehydroquinate synthase
B: 3-dehydroquinate synthase
C: 3-dehydroquinate synthase
D: 3-dehydroquinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,00821
Polymers164,4774
Non-polymers4,53117
Water6,630368
1
A: 3-dehydroquinate synthase
C: 3-dehydroquinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,51311
Polymers82,2392
Non-polymers2,2749
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-43 kcal/mol
Surface area27300 Å2
MethodPISA
2
B: 3-dehydroquinate synthase
D: 3-dehydroquinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,49510
Polymers82,2392
Non-polymers2,2568
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-35 kcal/mol
Surface area27810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.639, 60.825, 143.069
Angle α, β, γ (deg.)90.000, 93.750, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 233 or resid 239...
21(chain B and (resid 1 through 233 or resid 239...
31(chain C and (resid 1 through 233 or resid 239...
41(chain D and (resid 1 through 233 or resid 239 through 357))

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
11METMETASPASP(chain A and (resid 1 through 233 or resid 239...AA1 - 23314 - 246
12GLYGLYTHRTHR(chain A and (resid 1 through 233 or resid 239...AA239 - 306252 - 319
13METMETMETMET(chain A and (resid 1 through 233 or resid 239...AA311324
21METMETASPASP(chain B and (resid 1 through 233 or resid 239...BB1 - 23314 - 246
22GLYGLYTHRTHR(chain B and (resid 1 through 233 or resid 239...BB239 - 306252 - 319
23METMETMETMET(chain B and (resid 1 through 233 or resid 239...BB311 - 320324 - 333
24HISHISILEILE(chain B and (resid 1 through 233 or resid 239...BB332 - 357345 - 370
31METMETASPASP(chain C and (resid 1 through 233 or resid 239...CC1 - 23314 - 246
32GLYGLYTHRTHR(chain C and (resid 1 through 233 or resid 239...CC239 - 306252 - 319
33METMETMETMET(chain C and (resid 1 through 233 or resid 239...CC311 - 320324 - 333
34HISHISILEILE(chain C and (resid 1 through 233 or resid 239...CC332 - 357345 - 370
41METMETASPASP(chain D and (resid 1 through 233 or resid 239 through 357))DD1 - 23314 - 246
42GLYGLYILEILE(chain D and (resid 1 through 233 or resid 239 through 357))DD239 - 357252 - 370

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
3-dehydroquinate synthase / DHQS


Mass: 41119.258 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Providencia alcalifaciens F90-2004 (bacteria)
Gene: aroB, HMPREF1562_0140 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: X6Q997, 3-dehydroquinate synthase

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Non-polymers , 6 types, 385 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-7LH / (1R,3R,4S,5R)-3-[3-[3,4-bis(oxidanyl)phenyl]propanoyloxy]-1,4,5-tris(oxidanyl)cyclohexane-1-carboxylic acid


Mass: 356.325 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H20O9 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 mM Bis Tris Propane (pH 7.0) buffer, 200 mM MgCl2 and 28% polyethylene glycol 4000
PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.5→142.76 Å / Num. obs: 52941 / % possible obs: 98.8 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.04 / Rrim(I) all: 0.1 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.594.61.1282133546600.6060.581.2761.289.9
9.69-485.20.02751129770.9990.0120.0345.998.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimless0.6.2data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LLA

6lla


Resolution: 2.503→47.588 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2547 2676 5.06 %RANDOM
Rwork0.2053 50214 --
obs0.2079 52890 98.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.24 Å2 / Biso mean: 69.6599 Å2 / Biso min: 25.9 Å2
Refinement stepCycle: final / Resolution: 2.503→47.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10666 0 303 368 11337
Biso mean--74.82 58.72 -
Num. residues----1397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311172
X-RAY DIFFRACTIONf_angle_d0.80515191
X-RAY DIFFRACTIONf_chiral_restr0.0491787
X-RAY DIFFRACTIONf_plane_restr0.0051905
X-RAY DIFFRACTIONf_dihedral_angle_d8.536579
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6189X-RAY DIFFRACTION15.26TORSIONAL
12B6189X-RAY DIFFRACTION15.26TORSIONAL
13C6189X-RAY DIFFRACTION15.26TORSIONAL
14D6189X-RAY DIFFRACTION15.26TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.503-2.54810.35191370.3054226185
2.5481-2.59720.35831390.2953247094
2.5972-2.65020.3471360.2817263198
2.6502-2.70780.29011340.25232627100
2.7078-2.77080.31671390.24432657100
2.7708-2.840.31881310.24492636100
2.84-2.91680.3161400.23832705100
2.9168-3.00260.32481320.24652659100
3.0026-3.09950.32431550.25162636100
3.0995-3.21030.27691320.23452698100
3.2103-3.33880.28071380.22132642100
3.3388-3.49070.29891330.21422690100
3.4907-3.67470.27621480.21092646100
3.6747-3.90480.26031540.19162690100
3.9048-4.20610.21051510.17272674100
4.2061-4.62910.20181500.17182688100
4.6291-5.29820.22621430.17982699100
5.2982-6.67220.26411280.21122738100
6.6722-47.5880.20311560.1796276799

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