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- PDB-1shk: THE THREE-DIMENSIONAL STRUCTURE OF SHIKIMATE KINASE FROM ERWINIA ... -

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Basic information

Entry
Database: PDB / ID: 1shk
TitleTHE THREE-DIMENSIONAL STRUCTURE OF SHIKIMATE KINASE FROM ERWINIA CHRYSANTHEMI
ComponentsSHIKIMATE KINASE
KeywordsTRANSFERASE / 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
Biological speciesErwinia chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å
AuthorsKrell, T. / Coggins, J.R. / Lapthorn, A.J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and preliminary X-ray crystallographic analysis of shikimate kinase from Erwinia chrysanthemi.
Authors: Krell, T. / Coyle, J.E. / Horsburgh, M.J. / Coggins, J.R. / Lapthorn, A.J.
#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
DepositionOct 27, 1997Processing site: BNL
Revision 1.0Nov 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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)38,0245
Polymers37,9522
Non-polymers733
Water8,521473
1
A: SHIKIMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0243
Polymers18,9761
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SHIKIMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0002
Polymers18,9761
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: SHIKIMATE KINASE
hetero molecules

B: SHIKIMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0245
Polymers37,9522
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554y+1/2,-x+1/2,z-1/41
Buried area2100 Å2
ΔGint-25 kcal/mol
Surface area14350 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-18 kcal/mol
Surface area15520 Å2
MethodPISA
5
A: SHIKIMATE KINASE
B: SHIKIMATE KINASE
hetero molecules

A: SHIKIMATE KINASE
B: SHIKIMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,04910
Polymers75,9034
Non-polymers1466
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)108.500, 108.500, 92.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.497526, -0.860359, 0.110681), (-0.866844, 0.497881, -0.026385), (-0.032405, -0.10907, -0.993506)
Vector: 80.8, 48.6088, 31.7478)

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Components

#1: Protein SHIKIMATE KINASE


Mass: 18975.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Strain: NCPPB 1066 / Cellular location: CYTOPLASM / Gene: AROL / Plasmid: PTB361SK / Gene (production host): AROL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): (DE3) PLYSS / References: UniProt: P10880, shikimate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE GAP IN THE MOLECULAR STRUCTURE CORRESPONDS TO RESIDUES OF THE LID-DOMAIN. BY ANALOGY TO ...THE GAP IN THE MOLECULAR STRUCTURE CORRESPONDS TO RESIDUES OF THE LID-DOMAIN. BY ANALOGY TO ADENYLATE KINASES THE LID DOMAIN CLOSES OVER BOUND ATP.
Has protein modificationY

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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: 3.6 Å3/Da / Density % sol: 66 %
Crystal growpH: 6.9
Details: 2.16M NACL, 100MM HEPES BUFFER PH 6.9, 5MM ADP, 5MM SHIKIMATE, 10MM MGCL2
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl1drop
25 mMADP1drop
310 mM1dropMgCl2
416 mg/mlenzyme1drop
52.16 M1reservoirNaCl
6100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1996 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→24 Å / Num. obs: 44761 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 10
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.94 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELX-90model building
SHELX-90refinement
SHELX-90phasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→20 Å / σ(F): 0
Details: X-PLOR WAS USED FOR INITIAL ROUNDS OF REFINEMENT AND PROVIDED THE BULK SOLVENT CORRECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 4100 10 %RANDOM
Rwork0.176 ---
obs0.174 41323 99.4 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 3 473 2891

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