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- PDB-2q5r: Structure of apo Staphylococcus aureus D-tagatose-6-phosphate kinase -

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Basic information

Entry
Database: PDB / ID: 2q5r
TitleStructure of apo Staphylococcus aureus D-tagatose-6-phosphate kinase
ComponentsTagatose-6-phosphate kinase
KeywordsTRANSFERASE / D-tagatose-6-phosphate kinase / phosphoryl transfer / conformational change / kinase / lactose metabolism
Function / homology
Function and homology information


tagatose-6-phosphate kinase / lactose catabolic process via tagatose-6-phosphate / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity / ATP binding
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
Tagatose-6-phosphate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMcGrath, T.E. / Soloveychik, M. / Romanov, V. / Thambipillai, D. / Dharamsi, A. / Virag, C. / Domagala, M. / Pai, E.F. / Edwards, A.M. / Battaile, K. / Chirgadze, N.Y.
CitationJournal: TO BE PUBLISHED
Title: Structure of apo Staphylococcus aureus D-tagatose-6-phosphate kinase
Authors: McGrath, T.E. / Soloveychik, M. / Romanov, V. / Thambipillai, D. / Dharamsi, A. / Virag, C. / Domagala, M. / Pai, E.F. / Edwards, A.M. / Battaile, K. / Chirgadze, N.Y.
History
DepositionJun 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)144,7814
Polymers144,7814
Non-polymers00
Water8,989499
1
A: Tagatose-6-phosphate kinase
B: Tagatose-6-phosphate kinase


Theoretical massNumber of molelcules
Total (without water)72,3912
Polymers72,3912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-10 kcal/mol
Surface area27650 Å2
MethodPISA
2
C: Tagatose-6-phosphate kinase
D: Tagatose-6-phosphate kinase


Theoretical massNumber of molelcules
Total (without water)72,3912
Polymers72,3912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-7 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.952, 96.940, 94.485
Angle α, β, γ (deg.)90.00, 94.42, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is the dimer

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Components

#1: Protein
Tagatose-6-phosphate kinase / Phosphotagatokinase


Mass: 36195.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: ColA / Gene: lacC / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5HE12, tagatose-6-phosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350, 0.2M sodium thiocyanate, frozen in paratone, VAPOR DIFFUSION, SITTING DROP, temperature 100K, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 4, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. all: 146479 / Num. obs: 55270 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.078 / Χ2: 1.098 / Net I/σ(I): 15.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 5.4 / Num. unique all: 5686 / Χ2: 0.963 / % possible all: 93.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
JDirectordata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F02

2f02


Resolution: 2.3→14.99 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.88 / SU B: 15.622 / SU ML: 0.208 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.476 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2729 4.9 %RANDOM
Rwork0.215 ---
obs0.218 55227 90.09 %-
all-146479 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0.85 Å2
2---0.39 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9566 0 0 499 10065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229791
X-RAY DIFFRACTIONr_angle_refined_deg1.191.96813316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94251255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.68726.488447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.294151698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.981522
X-RAY DIFFRACTIONr_chiral_restr0.0720.21560
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027364
X-RAY DIFFRACTIONr_nbd_refined0.1880.24432
X-RAY DIFFRACTIONr_nbtor_refined0.2960.26620
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2593
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.212
X-RAY DIFFRACTIONr_mcbond_it0.4641.56422
X-RAY DIFFRACTIONr_mcangle_it0.77210017
X-RAY DIFFRACTIONr_scbond_it1.22833771
X-RAY DIFFRACTIONr_scangle_it1.9544.53289
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 213 -
Rwork0.23 3891 -
obs-4104 93.42 %
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)
11.1826-0.42930.6884.031-0.33911.32910.11430.0253-0.063-0.0979-0.03220.07520.2141-0.0659-0.0822-0.19130.0220.0534-0.1806-0.0229-0.15684.9251-17.272421.0816
24.12480.63380.65314.0677-0.47194.73020.1647-0.35170.21660.22360.06811.04190.0225-0.5896-0.2328-0.07820.00860.0261-0.0880.05260.1426-6.8518-32.241331.522
31.84931.73450.89923.67271.27412.1184-0.29680.01740.27-0.227-0.04350.3978-0.3186-0.01120.3403-0.16990.0462-0.0649-0.21720.0013-0.13437.551217.158722.6925
43.0054-0.7378-0.813.85152.44356.4737-0.52450.40360.3147-0.9257-0.28311.0742-0.9321-0.45340.80760.4430.006-0.5641-0.14160.03480.30020.271233.663210.8132
54.32220.31250.59230.98580.05054.4954-0.20130.9070.2495-0.28490.16770.081-0.09840.5970.0335-0.1785-0.07540.03870.06390.011-0.186444.36513.93195.7598
66.18061.38224.63536.84311.55547.5094-0.04330.9985-0.19910.43790.42690.87140.63030.4875-0.3836-0.02110.00070.11230.141-0.0287-0.038833.7857-7.68-8.3162
71.2008-0.12771.380.6045-0.46523.62940.02850.0409-0.02550.0611-0.0506-0.1074-0.0123-0.03180.0222-0.2378-0.00190.0391-0.18430.0021-0.191844.36440.629739.9019
85.0362.2885-0.95856.0437-0.11153.11850.16940.00930.57090.1037-0.09130.5794-0.2842-0.9063-0.078-0.14410.06130.05310.0748-0.0368-0.101632.73299.035856.5685
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 19321 - 213
2X-RAY DIFFRACTION2AA194 - 310214 - 330
3X-RAY DIFFRACTION3BB1 - 19321 - 213
4X-RAY DIFFRACTION4BB194 - 310214 - 330
5X-RAY DIFFRACTION5CC1 - 19321 - 213
6X-RAY DIFFRACTION6CC194 - 310214 - 330
7X-RAY DIFFRACTION7DD1 - 19321 - 213
8X-RAY DIFFRACTION8DD194 - 310214 - 330

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