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- PDB-4foo: Crystal Structure of Shikimate Dehydrogenase (aroE) Q237K Mutant ... -

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Basic information

Entry
Database: PDB / ID: 4foo
TitleCrystal Structure of Shikimate Dehydrogenase (aroE) Q237K Mutant from Helicobacter pylori
ComponentsShikimate dehydrogenase
KeywordsOXIDOREDUCTASE / shikimate / dehydrogenase / NADP Binding
Function / homology
Function and homology information


shikimate dehydrogenase (NADP+) / shikimate 3-dehydrogenase (NADP+) activity / shikimate metabolic process / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / NADP binding / cytosol
Similarity search - Function
Shikimate dehydrogenase / Shikimate dehydrogenase family / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / 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 speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsCheng, W.C. / Chen, T.J. / Wang, W.C.
History
DepositionJun 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Shikimate dehydrogenase
B: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)60,7652
Polymers60,7652
Non-polymers00
Water90150
1
A: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)30,3821
Polymers30,3821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)30,3821
Polymers30,3821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.808, 46.088, 119.078
Angle α, β, γ (deg.)90.000, 99.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Shikimate dehydrogenase


Mass: 30382.283 Da / Num. of mol.: 2 / Mutation: Q237K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: aroE, HP_1249 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: P56119, shikimate dehydrogenase (NADP+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M potassium acetate, 0.1M Tris, 23% PEG 3350 , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 6, 2012 / Details: mirrors
RadiationMonochromator: Si(111) Bent Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 16286 / % possible obs: 99.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.085 / Χ2: 1.048 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.55-2.6440.3124.915801.00999.9
2.64-2.7540.2635.816081.028100
2.75-2.8740.2256.916441.08199.9
2.87-3.0240.1788.516001.05999.9
3.02-3.213.90.12611.616221.06799.6
3.21-3.463.80.09414.416251.05399.9
3.46-3.813.90.07181641199.9
3.81-4.363.90.05324.816031.0699.5
4.36-5.483.90.05323.816551.04499.8
5.48-303.90.04827.817081.07999.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PHH

3phh


Resolution: 2.55→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.159 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 823 5.1 %RANDOM
Rwork0.1923 ---
obs0.1942 16234 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.6 Å2 / Biso mean: 26.2603 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å20 Å20.46 Å2
2---1.01 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4092 0 0 50 4142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224184
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9835630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3735518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33424.368174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.37615752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3171512
X-RAY DIFFRACTIONr_chiral_restr0.1050.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213094
X-RAY DIFFRACTIONr_mcbond_it0.9791.52590
X-RAY DIFFRACTIONr_mcangle_it1.84724132
X-RAY DIFFRACTIONr_scbond_it2.84831594
X-RAY DIFFRACTIONr_scangle_it4.5824.51498
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 56 -
Rwork0.201 1087 -
all-1143 -
obs--100 %

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