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- PDB-3nwj: Crystal structure of shikimate kinase from Arabidopsis thaliana (... -

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Basic information

Entry
Database: PDB / ID: 3nwj
TitleCrystal structure of shikimate kinase from Arabidopsis thaliana (AtSK2)
ComponentsAtSK2
KeywordsTRANSFERASE / P loop / shikimate / nucleoside monophosphate kinase / shikimate kinase / ATP binding / chloroplast
Function / homology
Function and homology information


shikimate kinase / shikimate kinase activity / shikimate metabolic process / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / chloroplast / magnesium ion binding / ATP binding
Similarity search - Function
Shikimate kinase, conserved site / Shikimate kinase signature. / Shikimate kinase/Threonine synthase-like 1 / Shikimate kinase/gluconokinase / Shikimate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Shikimate kinase 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsFucile, G. / Garcia, C. / Petit, P. / Christendat, D.
CitationJournal: Protein Sci. / Year: 2011
Title: Structural and biochemical investigation of two Arabidopsis shikimate kinases: The heat-inducible isoform is thermostable.
Authors: Fucile, G. / Garcia, C. / Carlsson, J. / Sunnerhagen, M. / Christendat, D.
History
DepositionJul 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AtSK2
B: AtSK2


Theoretical massNumber of molelcules
Total (without water)55,3172
Polymers55,3172
Non-polymers00
Water79344
1
A: AtSK2


Theoretical massNumber of molelcules
Total (without water)27,6591
Polymers27,6591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AtSK2


Theoretical massNumber of molelcules
Total (without water)27,6591
Polymers27,6591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-16 kcal/mol
Surface area18160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.378, 62.249, 40.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein AtSK2 / Putative shikimate kinase / At4g39540


Mass: 27658.516 Da / Num. of mol.: 2 / Fragment: UNP residues 55-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col-0 / Gene: At4g39540, At4g39540/F23K16_170 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8GY88, shikimate kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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 Å3/Da / Density % sol: 38.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 22% polyethylene glycol 3350, 0.2 M potassium fluoride, 3% 2-methyl-2,4-pentanediol, 1 mM magnesium chloride, 1 mM adenosine triphosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.35→19 Å / Num. obs: 16917 / % possible obs: 89.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.119 / Rsym value: 0.107 / Net I/σ(I): 13.3
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 5.1 / Rsym value: 0.56 / % possible all: 91.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2SHK

2shk


Resolution: 2.35→19 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 16.343 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.437 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 881 5.2 %RANDOM
Rwork0.19144 ---
obs0.19433 16021 87.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.974 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--1.31 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 0 44 3082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223092
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.721.9634164
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0865382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65123.651126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.04115576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9491518
X-RAY DIFFRACTIONr_chiral_restr0.120.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022242
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_it0.8921.51906
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70723058
X-RAY DIFFRACTIONr_scbond_it2.91731186
X-RAY DIFFRACTIONr_scangle_it4.7424.51106
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 66 -
Rwork0.214 1198 -
obs--90.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.29220.82250.11673.1265-0.27631.8034-0.0450.15930.2943-0.0891-0.02130.0375-0.27140.30130.06620.0616-0.0429-0.01420.21440.00710.044327.165-27.321-17.228
211.88880021.3172013.9076-0.6140.0908-0.65280.03610.0891-0.47260.1977-0.27170.52490.31470.12530.15470.3567-0.06740.151128.517-42.938-22.227
32.0040.3978-0.44082.38110.36654.6077-0.0239-0.1429-0.26530.1364-0.05480.00090.09220.16480.07870.0434-0.0125-0.01880.1923-0.02770.074632.783-35.651-11.38
42.8053-0.3867-2.10171.066-0.05046.9361-0.14930.00480.09860.3946-0.0053-0.0154-0.31530.36310.15460.2171-0.1254-0.01720.22110.01260.013437.131-21.819-4.904
53.8074-0.3234-0.03241.13570.44590.5521-0.00270.13060.2824-0.1188-0.06360.1423-0.0156-0.00750.06630.1262-0.0253-0.01110.03870.01090.09011.621-40.867-20.824
626.3982-7.82441.59574.4512-2.32162.19520.3546-0.66460.1103-0.172-0.2742-0.1084-0.09880.2477-0.08040.2261-0.02950.04980.2281-0.00010.125110.008-44.296-7.476
71.71740.3088-0.06051.93671.15263.9123-0.044-0.0758-0.16640.02420.0317-0.14230.25610.25150.01230.1022-0.0357-0.01590.11730.04540.09795.155-51.319-17.976
82.0792-0.7227-1.69052.33121.75516.0310.04870.1197-0.0164-0.088-0.15270.21610.1742-0.37310.10410.0948-0.0547-0.02820.08130.00470.0853-4.91-53.321-30.554
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A83 - 150
2X-RAY DIFFRACTION2A151 - 163
3X-RAY DIFFRACTION3A164 - 248
4X-RAY DIFFRACTION4A249 - 291
5X-RAY DIFFRACTION5B83 - 150
6X-RAY DIFFRACTION6B151 - 163
7X-RAY DIFFRACTION7B164 - 248
8X-RAY DIFFRACTION8B249 - 291

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