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- PDB-4fr5: Crystal Structure of Shikimate Dehydrogenase (aroE) Y210S Mutant ... -

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Basic information

Entry
Database: PDB / ID: 4fr5
TitleCrystal Structure of Shikimate Dehydrogenase (aroE) Y210S Mutant from Helicobacter pylori in Complex with Shikimate
ComponentsShikimate dehydrogenase
KeywordsOXIDOREDUCTASE / 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
Chem-SKM / Shikimate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCheng, W.C. / Chen, T.J. / Wang, W.C.
History
DepositionJun 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,9594
Polymers60,6102
Non-polymers3482
Water2,828157
1
A: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4792
Polymers30,3051
Non-polymers1741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4792
Polymers30,3051
Non-polymers1741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Shikimate dehydrogenase
hetero molecules

B: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9594
Polymers60,6102
Non-polymers3482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area2000 Å2
ΔGint-3 kcal/mol
Surface area23860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.507, 88.523, 118.185
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: 30305.139 Da / Num. of mol.: 2 / Mutation: Y210S
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


Mass: 174.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 38.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M sodium acetate, 0.1M Tris, 36% PEG 4000, pH 6.5, 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: Jun 10, 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: 2.2→30 Å / Num. obs: 25263 / % possible obs: 98.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.2-2.285.60.46242412195.6
2.28-2.375.60.4024.62412196.7
2.37-2.485.50.2986.12478198.2
2.48-2.615.50.22282496199
2.61-2.775.60.16310.62525199.5
2.77-2.995.70.12313.32508199.8
2.99-3.295.80.07521.52570199.9
3.29-3.765.80.05923.62549199.8
3.76-4.735.70.04730.32597199.5
4.73-305.60.03934.22716199

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PHG

3phg


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.626 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 1218 4.9 %RANDOM
Rwork0.1947 ---
obs0.1965 25076 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.99 Å2 / Biso mean: 29.6217 Å2 / Biso min: 5.19 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å20 Å2
2--3.38 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 24 157 4297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224234
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.9885702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8715524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.07824.545176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.95315760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0981512
X-RAY DIFFRACTIONr_chiral_restr0.1090.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213140
X-RAY DIFFRACTIONr_mcbond_it1.2921.52614
X-RAY DIFFRACTIONr_mcangle_it2.32624174
X-RAY DIFFRACTIONr_scbond_it3.39731620
X-RAY DIFFRACTIONr_scangle_it5.3814.51528
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 83 -
Rwork0.199 1661 -
all-1744 -
obs--94.83 %

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