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- PDB-2gpt: Crystal structure of Arabidopsis Dehydroquinate dehydratase-shiki... -

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Basic information

Entry
Database: PDB / ID: 2gpt
TitleCrystal structure of Arabidopsis Dehydroquinate dehydratase-shikimate dehydrogenase in complex with tartrate and shikimate
Components3-dehydroquinate dehydratase/ shikimate 5-dehydrogenase
KeywordsOXIDOREDUCTASE / LYASE / Type I dehydroquinate dehydratase / AroE / shikimate dehydrogenase / Arabidopsis thaliana / shikimate / tartrate / 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 / chloroplast stroma / aromatic amino acid family biosynthetic process / 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 / 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
Chem-SKM / L(+)-TARTARIC ACID / Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsSingh, S.A. / Christendat, D.
CitationJournal: Biochemistry / Year: 2006
Title: Structure of Arabidopsis dehydroquinate dehydratase-shikimate dehydrogenase and implications for metabolic channeling in the shikimate pathway
Authors: Singh, S.A. / Christendat, D.
History
DepositionApr 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

Downloads & links

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Assembly

Deposited unit
A: 3-dehydroquinate dehydratase/ shikimate 5-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6055
Polymers57,0891
Non-polymers5164
Water4,882271
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.934, 96.934, 116.157
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a monomer

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Components

#1: Protein 3-dehydroquinate dehydratase/ shikimate 5-dehydrogenase


Mass: 57088.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9SQT8, 3-dehydroquinate dehydratase, shikimate dehydrogenase (NADP+)
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-SKM / (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID / SHIKIMATE / Shikimic acid


Mass: 174.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.4 mM Sodium Tartrate tetrahydrate, 0.1 M tri-Sodium Citrate dihydrate pH5.6, 2.8 M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X8C10.9795
SYNCHROTRONNSLS X8C21.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.11
ReflectionResolution: 1.95→50 Å / Num. obs: 46428 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.044 / Net I/σ(I): 42.9
Reflection shellHighest resolution: 1.95 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.537 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
CAD4data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→28.46 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 279246.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1309 3 %RANDOM
Rwork0.232 ---
all0.229 ---
obs0.232 43932 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.1233 Å2 / ksol: 0.362598 e/Å3
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20.18 Å20 Å2
2---0.82 Å20 Å2
3---1.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.95→28.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3840 0 32 271 4143
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d2.88
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.582.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 170 2.5 %
Rwork0.292 6535 -
obs--87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protviv.paramprotviv.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4shk.paramtarviv.top
X-RAY DIFFRACTION5tarviv.paramshk.top

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