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- PDB-4fsh: Crystal Structure of Shikimate Dehydrogenase (aroE) Clinical Vari... -

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Basic information

Entry
Database: PDB / ID: 4fsh
TitleCrystal Structure of Shikimate Dehydrogenase (aroE) Clinical Variant v2356 from Helicobacter pylori in Complex with Shikimate
ComponentsShikimate dehydrogenase
KeywordsOXIDOREDUCTASE / 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: 2.85 Å
AuthorsCheng, W.C. / Chen, T.J. / Wang, W.C.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Shikimate Dehydrogenase (aroE) Clinical Variant v2356 from Helicobacter pylori in Complex with Shikimate
Authors: Cheng, W.C. / Chen, T.J. / Wang, W.C.
History
DepositionJun 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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

Downloads & links

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Assembly

Deposited unit
A: Shikimate dehydrogenase
B: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8493
Polymers60,6752
Non-polymers1741
Water73941
1
A: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5112
Polymers30,3371
Non-polymers1741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)30,3371
Polymers30,3371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.118, 71.870, 176.388
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: 30337.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: Helicobacter pylori 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


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


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.3 Å3/Da / Density % sol: 62.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.5M ammonium sulfate, 1.0M lithium sulfate, 0.1M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 19482 / % possible obs: 99.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.072 / Χ2: 1.059 / Net I/σ(I): 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.85-2.958.50.4644.918911.055100
2.95-3.078.50.3646.419091.085100
3.07-3.218.40.2299.819281.084100
3.21-3.388.50.13915.419031.06899.9
3.38-3.598.40.10419.519291.03799.9
3.59-3.878.40.08125.319351.09499.9
3.87-4.258.30.06529.819551.0599.9
4.25-4.878.10.05731.819491.03299.9
4.87-6.127.90.05831.519881.02999.9
6.12-307.30.03543.720951.05299.4

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Processing

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

3phg


Resolution: 2.85→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 1 / SU B: 13.491 / SU ML: 0.263 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.96 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26 971 5 %RANDOM
Rwork0.2143 ---
obs0.2166 19324 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 143.73 Å2 / Biso mean: 67.7202 Å2 / Biso min: 22.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å20 Å20 Å2
2--3.74 Å20 Å2
3----6.25 Å2
Refinement stepCycle: LAST / Resolution: 2.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4097 0 12 41 4150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224204
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9875659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6035520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21124.419172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.77815757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9161512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213109
X-RAY DIFFRACTIONr_mcbond_it1.0311.52600
X-RAY DIFFRACTIONr_mcangle_it2.01524152
X-RAY DIFFRACTIONr_scbond_it2.61831604
X-RAY DIFFRACTIONr_scangle_it4.5734.51507
LS refinement shellResolution: 2.85→2.923 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 54 -
Rwork0.284 1329 -
all-1383 -
obs--99.42 %

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