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- PDB-4fos: Crystal Structure of Shikimate Dehydrogenase (aroE) Q237A Mutant ... -

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Basic information

Entry
Database: PDB / ID: 4fos
TitleCrystal Structure of Shikimate Dehydrogenase (aroE) Q237A Mutant from Helicobacter pylori in Complex with Shikimate
ComponentsShikimate dehydrogenase
KeywordsOXIDOREDUCTASE / shikimate / dehydrogenase / NADP Binding
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 / 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
Chem-SKM / Shikimate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsCheng, W.C. / Chen, T.J. / Wang, W.C.
History
DepositionJun 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 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

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Assembly

Deposited unit
A: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4982
Polymers30,3241
Non-polymers1741
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.311, 62.718, 84.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Shikimate dehydrogenase /


Mass: 30324.182 Da / Num. of mol.: 1 / Mutation: Q237A
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: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.01 Å3/Da / Density % sol: 38.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M sodium acetate, 0.1M Tris, 36% PEG 4000 , 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: Apr 21, 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: 1.72→30 Å / Num. obs: 26472 / % possible obs: 99.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.046 / Χ2: 1.051 / Net I/σ(I): 16.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.72-1.786.60.2976.525531.09397.4
1.78-1.856.50.2298.525761.08498
1.85-1.946.50.16211.825761.09998.7
1.94-2.046.50.11415.725971.03999.3
2.04-2.176.50.0931926431.05299.9
2.17-2.336.70.07423.226551.01100
2.33-2.5770.05633.226471.066100
2.57-2.9470.05332.126721.025100
2.94-3.77.10.03844.827211.05499.9
3.7-306.80.0285628321.00399.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
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 3PHG

3phg


Resolution: 1.72→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.78 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1989 1338 5.1 %RANDOM
Rwork0.1717 ---
obs0.1731 26421 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.36 Å2 / Biso mean: 22.1107 Å2 / Biso min: 10.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.66 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.72→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 12 100 2172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222136
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9852882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5345268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53724.49489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29215381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.689156
X-RAY DIFFRACTIONr_chiral_restr0.270.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211590
X-RAY DIFFRACTIONr_mcbond_it1.6561.51318
X-RAY DIFFRACTIONr_mcangle_it2.8722107
X-RAY DIFFRACTIONr_scbond_it4.4213818
X-RAY DIFFRACTIONr_scangle_it7.0534.5773
LS refinement shellResolution: 1.721→1.766 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 86 -
Rwork0.199 1782 -
all-1868 -
obs--96.94 %

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