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- PDB-2o7q: Crystal Structure of the A. thaliana DHQ-dehydroshikimate-SDH-shi... -

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Basic information

Entry
Database: PDB / ID: 2o7q
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 metabolic process / shikimate 3-dehydrogenase (NADP+) activity / embryo development ending in seed dormancy / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / chloroplast stroma / amino acid biosynthetic process ...shikimate dehydrogenase (NADP+) / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / embryo development ending in seed dormancy / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / chloroplast stroma / 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 / Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 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

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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)57,7576
Polymers57,1211
Non-polymers6365
Water2,954164
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)115,51512
Polymers114,2422
Non-polymers1,27310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area5600 Å2
ΔGint-88 kcal/mol
Surface area37720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.611, 96.611, 115.945
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.4M potassium sodium tartrate, 2.4M ammonium sulfate, 0.1M tri-sodium citrate dihydrate (pH5.6), 1mM shikimate, 50 mM dehydroquinate soaked in, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9807 Å / Relative weight: 1
ReflectionResolution: 1.77→30 Å / Num. obs: 51079 / Redundancy: 3.8 % / Rsym value: 0.062

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Processing

Software
NameClassification
HKL-3000data collection
SOLVEphasing
CNSrefinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflectionSelection details
Rfree0.2138 -random
obs0.2593 51079 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.556 Å20 Å20 Å2
2--2.556 Å20 Å2
3----5.112 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3864 0 38 164 4066
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.911.5
X-RAY DIFFRACTIONc_mcangle_it2.8082
X-RAY DIFFRACTIONc_scbond_it3.1032
X-RAY DIFFRACTIONc_scangle_it4.0952.5

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