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- PDB-1e6c: K15M MUTANT OF SHIKIMATE KINASE FROM ERWINIA CHRYSANTHEMI -

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Basic information

Entry
Database: PDB / ID: 1e6c
TitleK15M MUTANT OF SHIKIMATE KINASE FROM ERWINIA CHRYSANTHEMI
ComponentsSHIKIMATE KINASE
KeywordsTRANSFERASE / MUTANT SHIKIMATE KINASE / PHOSPHORYL TRANSFER / ADP / SHIKIMATE PATHWAY / P-LOOP PROTEIN
Function / homology
Function and homology information


shikimate kinase / shikimate kinase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Shikimate kinase 2 / Shikimate kinase, conserved site / Shikimate kinase signature. / Shikimate kinase/Threonine synthase-like 1 / Shikimate kinase/gluconokinase / Shikimate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Shikimate kinase 2
Similarity search - Component
Biological speciesERWINIA CHRYSANTHEMI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMaclean, J. / Krell, T. / Coggins, J.R. / Lapthorn, A.J.
Citation
Journal: Protein Sci. / Year: 2001
Title: Biochemical and X-Ray Crystallographic Studies on Shikimate Kinase: The Important Structural Role of the P-Loop Lysine
Authors: Krell, T. / Maclean, J. / Boam, D.J. / Cooper, A. / Resmini, M. / Brocklehurst, K. / Kelly, S.M. / Price, N.C. / Lapthorn, A.J. / Coggins, J.R.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: The Three-Dimensional Structure of Shikimate Kinase
Authors: Krell, T. / Coggins, J.R. / Lapthorn, A.J.
History
DepositionAug 10, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 KINASE
B: SHIKIMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,95812
Polymers37,9882
Non-polymers97010
Water3,855214
1
A: SHIKIMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4796
Polymers18,9941
Non-polymers4855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SHIKIMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4796
Polymers18,9941
Non-polymers4855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.860, 106.940, 42.750
Angle α, β, γ (deg.)90.00, 119.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.50176, 0.00043, -0.86501), (0.00111, -1, -0.00114), (-0.86501, -0.00153, 0.50176)
Vector: 32.16613, 26.49718, 18.53906)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SHIKIMATE KINASE


Mass: 18993.812 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ERWINIA CHRYSANTHEMI (bacteria) / Gene: AROL / Plasmid: PTB361SK / Gene (production host): AROL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10880, shikimate kinase

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Non-polymers , 5 types, 224 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCHAIN A, B ENGINEERED MUTATION LYS15MET ENZYME REACTION: ATP + SHIKIMATE = ADP + SHIKIMATE 3- ...CHAIN A, B ENGINEERED MUTATION LYS15MET ENZYME REACTION: ATP + SHIKIMATE = ADP + SHIKIMATE 3-PHOSPHATE. INVOLVED IN THE BIOSYNTHESIS OF AROMATIC AMINO ACIDS
Sequence detailsREFERENCE: THE SEQUENCE IS DESCRIBED IN MINTON N.P., WHITEHEAD P.J., ATKINSON T., GILBERT H.J. ...REFERENCE: THE SEQUENCE IS DESCRIBED IN MINTON N.P., WHITEHEAD P.J., ATKINSON T., GILBERT H.J. NUCLEIC ACIDS RES. 17:1769-1769(1989).

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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: 2.24 Å3/Da / Density % sol: 44.6 %
Crystal growpH: 8
Details: 10% PEG8000, 100MM TRIS/HCL BUFFER PH 8.0, 2.5MM ADP, 2.5MM SHIKIMATE, 10MM MGCL2
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-10 mg/mlprotein1drop
210 %PEG80001reservoir
3100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 1998 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→21.4 Å / Num. obs: 27407 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 19.073 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 15
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.348 / % possible all: 69.1
Reflection
*PLUS
Num. measured all: 164162
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 69 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SHK

1shk


Resolution: 1.8→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16471 / ESU R Free: 0.14659
Details: HYDROGEN ATOM CONTRIBUTION AND EXTERNAL BULK SOLVENT CORRECTION WERE APPLIED AS FPART . THE SPACE GROUP ASSIGNMENT WAS EXTREMELY CLOSE BETWEEN P21 AND C2221. IT WAS DECIDED TO PROCEED WITH ...Details: HYDROGEN ATOM CONTRIBUTION AND EXTERNAL BULK SOLVENT CORRECTION WERE APPLIED AS FPART . THE SPACE GROUP ASSIGNMENT WAS EXTREMELY CLOSE BETWEEN P21 AND C2221. IT WAS DECIDED TO PROCEED WITH P21 AND USE STRICT NCS RESTRAINTS BETWEEN MONOMERS.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1551 5 %RANDOM
Rwork0.188 ---
obs-30838 93 %-
Displacement parametersBiso mean: 23.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2610 0 60 214 2884
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6232
X-RAY DIFFRACTIONp_mcangle_it2.313
X-RAY DIFFRACTIONp_scbond_it2.2422
X-RAY DIFFRACTIONp_scangle_it3.5763
X-RAY DIFFRACTIONp_plane_restr0.0210.03
X-RAY DIFFRACTIONp_chiral_restr0.1250.15
X-RAY DIFFRACTIONp_singtor_nbd0.1840.3
X-RAY DIFFRACTIONp_multtor_nbd0.2650.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1730.3
X-RAY DIFFRACTIONp_planar_tor47
X-RAY DIFFRACTIONp_staggered_tor16.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor36.420
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

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