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- PDB-2jg1: STRUCTURE OF Staphylococcus aureus D-TAGATOSE-6-PHOSPHATE KINASE ... -

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Basic information

Entry
Database: PDB / ID: 2jg1
TitleSTRUCTURE OF Staphylococcus aureus D-TAGATOSE-6-PHOSPHATE KINASE with cofactor and substrate
ComponentsTAGATOSE-6-PHOSPHATE KINASE
KeywordsTRANSFERASE / D-TAGATOSE-6-PHOSPHATE KINASE / PHOSPHORYL TRANSFER / CONFORMATIONAL CHANGES / KINASE / LACTOSE METABOLISM
Function / homology
Function and homology information


tagatose-6-phosphate kinase / phosphofructokinase activity / lactose catabolic process via tagatose-6-phosphate / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity / ATP binding / cytosol
Similarity search - Function
Tagatose-6-phosphate kinase / Tagatose/fructose phosphokinase / pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase ...Tagatose-6-phosphate kinase / Tagatose/fructose phosphokinase / pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 6-O-phosphono-beta-D-tagatofuranose / Tagatose-6-phosphate kinase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMiallau, L. / Hunter, W.N. / McSweeney, S.M. / Leonard, G.A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structures of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase Implicate Domain Motions in Specificity and Mechanism.
Authors: Miallau, L. / Hunter, W.N. / Mcsweeney, S.M. / Leonard, G.A.
History
DepositionFeb 7, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TAGATOSE-6-PHOSPHATE KINASE
B: TAGATOSE-6-PHOSPHATE KINASE
C: TAGATOSE-6-PHOSPHATE KINASE
D: TAGATOSE-6-PHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,70714
Polymers145,3014
Non-polymers2,40610
Water15,763875
1
A: TAGATOSE-6-PHOSPHATE KINASE
D: TAGATOSE-6-PHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7116
Polymers72,6502
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-35.82 kcal/mol
Surface area26840 Å2
MethodPISA
2
B: TAGATOSE-6-PHOSPHATE KINASE
C: TAGATOSE-6-PHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9968
Polymers72,6502
Non-polymers1,3456
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-43.82 kcal/mol
Surface area25910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.200, 97.090, 154.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9903, -0.02375, 0.13686), (0.04733, -0.98401, 0.17171), (0.1306, 0.17652, 0.97559)28.38305, 75.51431, -8.45021
2given(0.07907, 0.99274, -0.09069), (-0.99381, 0.07138, -0.08516), (-0.07807, 0.09686, 0.99223)-14.09521, 76.27168, -40.48796

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Components

#1: Protein
TAGATOSE-6-PHOSPHATE KINASE / PHOSPHOTAGATOKINASE


Mass: 36325.184 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: NCTC 8325 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A0B9, tagatose-6-phosphate kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Sugar ChemComp-TA6 / 6-O-phosphono-beta-D-tagatofuranose / 6-O-phosphono-beta-D-tagatose / 6-O-phosphono-D-tagatose / 6-O-phosphono-tagatose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 875 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 124 TO MSE ENGINEERED RESIDUE IN CHAIN A, LEU 125 TO MSE ...ENGINEERED RESIDUE IN CHAIN A, LEU 124 TO MSE ENGINEERED RESIDUE IN CHAIN A, LEU 125 TO MSE ENGINEERED RESIDUE IN CHAIN B, LEU 124 TO MSE ENGINEERED RESIDUE IN CHAIN B, LEU 125 TO MSE ENGINEERED RESIDUE IN CHAIN C, LEU 124 TO MSE ENGINEERED RESIDUE IN CHAIN C, LEU 125 TO MSE ENGINEERED RESIDUE IN CHAIN D, LEU 124 TO MSE ENGINEERED RESIDUE IN CHAIN D, LEU 125 TO MSE
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: 2.3 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.5
Details: 0.2 M MAGNESIUM ACETATE TETRAHYDRATE, 0.1 M SODIUM CACODYLATE PH 6.5, 10% PEG 8000, 15% PEG 550, 10 MM ATP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→24.8 Å / Num. obs: 96948 / % possible obs: 99.8 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.6
Reflection shellResolution: 2→2.12 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SHARPmodel building
XSCALEdata scaling
XPREPphasing
SHELXDphasing
SHELXEphasing
SHARPphasing
REFMAC5.3.0011refinement
RefinementMethod to determine structure: SAD / Resolution: 2→24.85 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.131 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 4857 5 %RANDOM
Rwork0.19 ---
obs0.192 92089 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→24.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9701 0 145 875 10721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210202
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.98213918
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7151292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.1526.531467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.549151769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0571523
X-RAY DIFFRACTIONr_chiral_restr0.0760.21620
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027627
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1860.24453
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.26894
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2875
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0720.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6631.56562
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.047210280
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.48234084
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2674.53622
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 333 -
Rwork0.232 6523 -
obs--97.55 %

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