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- PDB-2o7s: Crystal Structure of the A. thaliana DHQ-dehydroshikimate-SDH-shi... -

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Basic information

Entry
Database: PDB / ID: 2o7s
TitleCrystal Structure of the A. thaliana DHQ-dehydroshikimate-SDH-shikimate-NADP(H)
ComponentsBifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase
KeywordsOXIDOREDUCTASE / TRANSFERASE / Shikimate / NADPH / dehydroshikimate / bifunctional enzyme
Function / homology
Function and homology information


shikimate dehydrogenase (NADP+) / shikimate 3-dehydrogenase (NADP+) activity / shikimate metabolic process / embryo development ending in seed dormancy / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / chloroplast stroma / aromatic amino acid family biosynthetic process / amino acid biosynthetic process ...shikimate dehydrogenase (NADP+) / shikimate 3-dehydrogenase (NADP+) activity / shikimate metabolic process / embryo development ending in seed dormancy / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / chloroplast stroma / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / chloroplast / NADP binding
Similarity search - Function
Shikimate dehydrogenase / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / Shikimate dehydrogenase family / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain ...Shikimate dehydrogenase / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / Shikimate dehydrogenase family / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / Aldolase class I / Aldolase-type TIM barrel / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-DEHYDROSHIKIMATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L(+)-TARTARIC ACID / Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.78 Å
AuthorsChristendat, D. / Singh, S.A.
CitationJournal: Cryst.Growth Des. / Year: 2007
Title: The DHQ-dehydroshikimate-SDH-shikimate-NADP(H) Complex: Insights into Metabolite Transfer in the Shikimate Pathway
Authors: Singh, S.A. / Christendat, D.
History
DepositionDec 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4596
Polymers57,1211
Non-polymers1,3385
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase
hetero molecules

A: Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,91812
Polymers114,2422
Non-polymers2,67610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area8100 Å2
ΔGint-33 kcal/mol
Surface area37260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.447, 97.447, 116.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase / E.C.1.1.1.25, E.C.4.2.1.10 / Dehydroquinase-Shikimate Dehydrogenase / DHQ-SDH protein / DHQase-SORase


Mass: 57120.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: contains Dehydroquinate dehydratase (EC 4.2.1.10) and Shikimate dehydrogenase (EC 1.1.1.25)
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Gene: EMB3004 / Plasmid: pET28 with C-terminal His tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon+
References: UniProt: Q9SQT8, shikimate dehydrogenase (NADP+), 3-dehydroquinate dehydratase

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Non-polymers , 5 types, 210 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DHK / 3-DEHYDROSHIKIMATE


Mass: 174.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O5
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCOMPOUND DEHYDROSHIKIMATE DHK 9241 AND TARTRATE TLA 1241 OCCUPY THE SAME SITE. DEHYDROSHIKIMATE IS ...COMPOUND DEHYDROSHIKIMATE DHK 9241 AND TARTRATE TLA 1241 OCCUPY THE SAME SITE. DEHYDROSHIKIMATE IS COVALENTLY BONDED TO LYS 241
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.4M K-Na-tartrate, 0.1M sodium citrate (pH 5.6), 2.4M ammonium sulfate, 1 mM shikimate, 33 mM NADP+ soak , VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9807 Å
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9807 Å / Relative weight: 1
ReflectionResolution: 1.78→30 Å / Num. obs: 61503 / Redundancy: 5.1 % / Rsym value: 0.054

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Processing

Software
NameClassification
HKL-3000data collection
CNSrefinement
HKL-3000data reduction
HKL-3000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.78→30 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2334 -random
obs0.2688 61503 -
Refinement stepCycle: LAST / Resolution: 1.78→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3850 0 86 205 4141
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.8061.5
X-RAY DIFFRACTIONc_mcangle_it2.4422
X-RAY DIFFRACTIONc_scbond_it2.692
X-RAY DIFFRACTIONc_scangle_it3.6022.5

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