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- PDB-3doo: Crystal structure of shikimate dehydrogenase from Staphylococcus ... -

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Basic information

Entry
Database: PDB / ID: 3doo
TitleCrystal structure of shikimate dehydrogenase from Staphylococcus epidermidis complexed with shikimate
ComponentsShikimate dehydrogenase
KeywordsOXIDOREDUCTASE / alpha-beta structure / Rossmann fold / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / NADP
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
Similarity search - Function
Shikimate dehydrogenase / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / Shikimate dehydrogenase family / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily ...Shikimate dehydrogenase / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / Shikimate dehydrogenase family / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / 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 speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHan, C. / Hu, T. / Wu, D. / Zhou, J. / Shen, X. / Qu, D. / Jiang, H.
CitationJournal: Febs J. / Year: 2009
Title: X-ray crystallographic and enzymatic analyses of shikimate dehydrogenase from Staphylococcus epidermidis
Authors: Han, C. / Hu, T. / Wu, D. / Qu, S. / Zhou, J. / Ding, J. / Shen, X. / Qu, D. / Jiang, H.
History
DepositionJul 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Nov 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

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Assembly

Deposited unit
A: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2242
Polymers31,0501
Non-polymers1741
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.189, 52.529, 56.777
Angle α, β, γ (deg.)90.000, 96.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Shikimate dehydrogenase


Mass: 31050.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: RP62A / Gene: aroE / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5HNV1, 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.: 151 / 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: 2.16 Å3/Da / Density % sol: 43 % / Mosaicity: 0.79 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium Cacodylate pH 6.5, 23% PEG 8000, 0.2M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→28.23 Å / Num. obs: 13476 / % possible obs: 99.2 % / Redundancy: 3.52 % / Rmerge(I) obs: 0.122 / Χ2: 1.32 / Net I/σ(I): 5.2 / Scaling rejects: 2505
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.2-2.283.450.381.9467413471.0299.6
2.28-2.373.640.3642.1490913401.1199.9
2.37-2.483.620.3322.3495613521.1599.8
2.48-2.613.630.3042.5495613431.1799.9
2.61-2.773.610.253497713451.1999.9
2.77-2.993.610.2153.5512013771.3699.9
2.99-3.293.530.1534.9498313371.699.9
3.29-3.763.410.0957.5507013471.6999.4
3.76-4.733.410.05911.9512413551.5398.9
4.73-28.233.290.04614.2515513331.495

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Processing

Software
NameVersionClassificationNB
d*TREK7.1SSIdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DON

3don


Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.889 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.563 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.312 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 668 5 %RANDOM
Rwork0.188 ---
obs0.192 13461 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.43 Å2 / Biso mean: 28.345 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å2-0.22 Å2
2--1.53 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 12 151 2199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222089
X-RAY DIFFRACTIONr_angle_refined_deg2.0821.9572835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8285256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.75225.63894
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.81915367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.144156
X-RAY DIFFRACTIONr_chiral_restr0.1380.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021556
X-RAY DIFFRACTIONr_nbd_refined0.2390.21022
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21446
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2119
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.29
X-RAY DIFFRACTIONr_mcbond_it1.2061.51331
X-RAY DIFFRACTIONr_mcangle_it1.93722086
X-RAY DIFFRACTIONr_scbond_it3.0763873
X-RAY DIFFRACTIONr_scangle_it4.6034.5749
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 48 -
Rwork0.218 935 -
all-983 -
obs-983 99.8 %

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