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- PDB-2jg5: CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOFRUCTOKINASE FROM STAPHYLO... -

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Basic information

Entry
Database: PDB / ID: 2jg5
TitleCRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOFRUCTOKINASE FROM STAPHYLOCOCCUS AUREUS
ComponentsFRUCTOSE 1-PHOSPHATE KINASE
KeywordsTRANSFERASE / KINASE / 1-PHOSPHOFRUCTOKINASE
Function / homology
Function and homology information


1-phosphofructokinase activity / lactose metabolic process / tagatose-6-phosphate kinase / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity / ATP binding
Similarity search - Function
Fructose 1-phosphate kinase / Tagatose/fructose phosphokinase / 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
AuthorsYan, X. / Carter, L.G. / Johnson, K.A. / Liu, H. / Dorward, M. / McMahon, S.A. / Oke, M. / Powers, H. / Coote, P.J. / Naismith, J.H.
CitationJournal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
History
DepositionFeb 8, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 28, 2011Group: Database references / Derived calculations / Structure summary
Revision 1.3Mar 11, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 13, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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: FRUCTOSE 1-PHOSPHATE KINASE
B: FRUCTOSE 1-PHOSPHATE KINASE


Theoretical massNumber of molelcules
Total (without water)65,1112
Polymers65,1112
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-20 kcal/mol
Surface area25550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.010, 160.260, 40.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETASNASN4AA1 - 81 - 8
211METMETASNASN4BB1 - 81 - 8
112LYSLYSGLYGLY4AA38 - 6138 - 61
212LYSLYSGLYGLY4BB38 - 6138 - 61
122PROPROVALVAL4AA106 - 159106 - 159
222PROPROVALVAL4BB106 - 159106 - 159
132ALAALALEULEU4AA167 - 176167 - 176
232ALAALALEULEU4BB167 - 176167 - 176
142TYRTYRTHRTHR4AA202 - 279202 - 279
242TYRTYRTHRTHR4BB202 - 279202 - 279
152THRTHRGLNGLN4AA287 - 297287 - 297
252THRTHRGLNGLN4BB287 - 297287 - 297
162PROPROILEILE4AA63 - 6863 - 68
262PROPROILEILE4BB63 - 6863 - 68
172THRTHRILEILE4AA70 - 8170 - 81
272THRTHRILEILE4BB70 - 8170 - 81
113PHEPHEPHEPHE4AA177 - 189177 - 189
213PHEPHEPHEPHE4BB177 - 189177 - 189
114VALVALGLYGLY4AA298 - 305298 - 305
214VALVALGLYGLY4BB298 - 305298 - 305
115ILEILELEULEU5AA89 - 9389 - 93
215ILEILELEULEU5BB89 - 9389 - 93
125GLUGLUGLYGLY5AA98 - 10598 - 105
225GLUGLUGLYGLY5BB98 - 10598 - 105
116ASPASPPHEPHE5AA12 - 1612 - 16
216ASPASPPHEPHE5BB12 - 1612 - 16
126ASNASNTYRTYR5AA26 - 3226 - 32
226ASNASNTYRTYR5BB26 - 3226 - 32

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper: (Code: given
Matrix: (-0.99808, -0.00574, -0.06161), (0.00015, -0.99591, 0.09033), (-0.06188, 0.09015, 0.994)
Vector: 1.09623, 158.3727, -8.1911)

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Components

#1: Protein FRUCTOSE 1-PHOSPHATE KINASE


Mass: 32555.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: MRSA252 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KWK1, 1-phosphofructokinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.04 Å3/Da / Density % sol: 40 %
Crystal growpH: 5.6
Details: 0.2 M AMMONIUM ACETATE, 0.1M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 30% W/V PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 5, 2006 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.28→30 Å / Num. obs: 25486 / % possible obs: 98.1 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.65
Reflection shellResolution: 2.28→2.42 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 11.65 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ABQ

2abq


Resolution: 2.3→19.75 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.87 / SU B: 20.902 / SU ML: 0.247 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.468 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1290 5.1 %RANDOM
Rwork0.212 ---
obs0.215 24100 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4572 0 0 130 4702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224634
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9646294
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89226.559186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9915792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6711510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023424
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.22222
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.23296
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.289
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3811.53094
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.64424910
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.99431679
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.584.51384
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
168medium positional0.130.5
21418medium positional0.310.5
3112medium positional0.210.5
455medium positional0.350.5
552medium positional0.140.5
648medium positional0.150.5
545loose positional0.585
653loose positional0.835
168medium thermal0.372
21418medium thermal0.472
3112medium thermal0.482
455medium thermal0.32
552medium thermal0.262
648medium thermal0.42
545loose thermal0.6910
653loose thermal1.2910
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 75 -
Rwork0.279 1649 -
obs--94.57 %
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)
13.28350.1767-0.57934.52630.49171.0392-0.0217-0.04350.0050.32720.04960.6096-0.0214-0.16-0.0279-0.0944-0.0097-0.045-0.10620.0325-0.11868.848568.116812.1645
21.1677-0.3673-0.88213.92841.50251.0973-0.03550.16760.0206-0.22910.0836-0.1110.02730.0443-0.0481-0.0745-0.0147-0.0697-0.06170.0194-0.098320.404955.92323.2341
31.8704-1.18330.0157.5555-0.0971.0313-0.2582-0.04480.05190.33850.2257-0.45720.00190.33740.0325-0.1138-0.02910.0174-0.0283-0.0432-0.1015-8.669391.66368.9124
40.7557-0.64290.70922.5771-1.19871.2507-0.020.20570.0891-0.2258-0.0396-0.1240.01250.10940.0596-0.0492-0.02830.0639-0.0068-0.0308-0.1042-20.1567103.5395-1.2351
56.33230.3368-0.20363.2722-1.1213.8352-0.24670.9322-0.5371-0.46270.11230.07490.2531-0.16990.1344-0.0178-0.07660.01020.0184-0.1094-0.0713-0.479973.4024-6.9891
68.09060.9373-2.79952.05540.83652.88830.01481.00210.1679-0.35310.0524-0.0531-0.1251-0.1571-0.0672-0.0213-0.02930.0214-0.00560.0219-0.13133.202682.2362-7.6529
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9
2X-RAY DIFFRACTION1A38 - 88
3X-RAY DIFFRACTION2A106 - 306
4X-RAY DIFFRACTION3B1 - 9
5X-RAY DIFFRACTION3B38 - 88
6X-RAY DIFFRACTION4B106 - 306
7X-RAY DIFFRACTION5A10 - 37
8X-RAY DIFFRACTION5A89 - 105
9X-RAY DIFFRACTION6B10 - 37
10X-RAY DIFFRACTION6B89 - 105

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