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

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Basic information

Entry
Database: PDB / ID: 3don
TitleCrystal structure of shikimate dehydrogenase from Staphylococcus epidermidis
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
Shikimate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 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: Non-polymer description / Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)31,1422
Polymers31,0501
Non-polymers921
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.877, 54.153, 102.724
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: 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.06 % / Mosaicity: 0.49 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1M tri-Sodium Citrate dihydrate pH 5.8, 24% PEG 4000, 0.2M Ammonium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONPhoton Factory BL-6A20.97901, 0.97953, 0.96429
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEJan 5, 2008
ADSC QUANTUM 4r2CCDMar 7, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.979011
30.979531
40.964291
ReflectionResolution: 2.1→47.9 Å / Num. obs: 17458 / % possible obs: 97.9 % / Redundancy: 5.57 % / Rmerge(I) obs: 0.1 / Χ2: 1.16 / Net I/σ(I): 5.9 / Scaling rejects: 5184
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.82 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2 / Num. measured all: 10094 / Num. unique all: 1714 / Χ2: 0.79 / % possible all: 98.8

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Processing

Software
NameVersionClassificationNB
d*TREK7.1SSIdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
d*TREKdata reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.885 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.847 / SU B: 4.98 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 896 5.2 %RANDOM
Rwork0.183 ---
obs0.187 17384 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.18 Å2 / Biso mean: 23.175 Å2 / Biso min: 6.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2--1.19 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 6 222 2312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222139
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.9532902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3075264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.26325.71498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86915378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.643156
X-RAY DIFFRACTIONr_chiral_restr0.1340.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021594
X-RAY DIFFRACTIONr_nbd_refined0.2080.2924
X-RAY DIFFRACTIONr_nbtor_refined0.30.21440
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.290.2149
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.213
X-RAY DIFFRACTIONr_mcbond_it1.1111.51373
X-RAY DIFFRACTIONr_mcangle_it1.7522140
X-RAY DIFFRACTIONr_scbond_it2.6563885
X-RAY DIFFRACTIONr_scangle_it3.7764.5761
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 64 -
Rwork0.23 1176 -
all-1240 -
obs-1240 98.49 %

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