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- PDB-3phi: Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori in comp... -

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Basic information

Entry
Database: PDB / ID: 3phi
TitleShikimate 5-Dehydrogenase (aroE) from Helicobacter pylori in complex with Shikimate and NADPH
ComponentsShikimate dehydrogenase
KeywordsOXIDOREDUCTASE / shikimate dehydrogenase / shikimate pathway / Helicobacter pylori / alpha/beta domain / Rossmann fold
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
Chem-NDP / Chem-SKM / Shikimate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsCheng, W.C. / Lin, S.C. / Wang, W.C.
CitationJournal: To be Published
Title: Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori in complex with Shikimate and NADPH
Authors: Cheng, W.C. / Lin, S.C. / Wang, W.C.
History
DepositionNov 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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)62,1176
Polymers60,2782
Non-polymers1,8394
Water2,972165
1
A: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0593
Polymers30,1391
Non-polymers9202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0593
Polymers30,1391
Non-polymers9202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.990, 48.391, 123.002
Angle α, β, γ (deg.)90.00, 97.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Shikimate dehydrogenase /


Mass: 30138.961 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C7H10O5
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG 8000, 0.1M BIS-TRIS, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.04→30 Å / Num. obs: 32329 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 32.2
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 10.3 / Num. unique all: 2979 / Rsym value: 0.131 / % possible all: 90.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.4.0077refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PHG

3phg


Resolution: 2.04→28.23 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: THROUGHOUT / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23124 1646 5.1 %RANDOM
Rwork0.20774 ---
obs0.20896 30682 96.17 %-
all-32345 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.245 Å2
Baniso -1Baniso -2Baniso -3
1-4.15 Å20 Å2-0.91 Å2
2---2.18 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 2.04→28.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 120 165 4339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224273
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6562.0175773
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9455514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63724.451173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00115744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7361512
X-RAY DIFFRACTIONr_chiral_restr0.1120.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0213128
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9311.52570
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.15624100
X-RAY DIFFRACTIONr_scbond_it4.97531703
X-RAY DIFFRACTIONr_scangle_it7.3064.51673
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.043→2.096 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 102 -
Rwork0.208 1873 -
obs--80.35 %

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