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- PDB-4omu: Crystal structure of shikimate dehydrogenase (AroE) from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 4omu
TitleCrystal structure of shikimate dehydrogenase (AroE) from Pseudomonas putida
ComponentsShikimate dehydrogenase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


shikimate dehydrogenase (NADP+) / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / 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 / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / Leucine Dehydrogenase, chain A, domain 1 / NAD(P)-binding Rossmann-like 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 / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / Leucine Dehydrogenase, chain A, domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Shikimate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPeek, J. / Christendat, D.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of shikimate dehydrogenase (AroE) from Pseudomonas putida
Authors: Peek, J. / Christendat, D.
History
DepositionJan 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Shikimate dehydrogenase
B: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9273
Polymers60,8312
Non-polymers961
Water8,989499
1
A: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)30,4161
Polymers30,4161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5122
Polymers30,4161
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-24 kcal/mol
Surface area22620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.555, 84.393, 94.404
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Shikimate dehydrogenase


Mass: 30415.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: aroE-1, aroE, aroE1, PP_0074 / Production host: Escherichia coli (E. coli)
References: UniProt: Q88RQ5, shikimate dehydrogenase (NADP+)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.1M NaHEPES, 2M Ammonium Sulfate, 2% PEG400, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.65→47.2 Å / Num. all: 65692 / Num. obs: 64531 / % possible obs: 98.2 % / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Rmerge(I) obs: 0.056 / Rsym value: 0.046 / Net I/σ(I): 33.4

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P77

1p77


Resolution: 1.65→47.2 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 1925 3.1 %RANDOM
Rwork0.1811 ---
all-62102 --
obs-60177 --
Refinement stepCycle: LAST / Resolution: 1.65→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4196 0 5 499 4700
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d1.1155
X-RAY DIFFRACTIONp_bond_d0.007

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