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- PDB-3ct4: Structure of Dha-kinase subunit DhaK from L. Lactis -

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Basic information

Entry
Database: PDB / ID: 3ct4
TitleStructure of Dha-kinase subunit DhaK from L. Lactis
ComponentsPTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
KeywordsTRANSFERASE / PTS dependent / dihydroxyacetone kinase subunit / tranferase / covalently linked 2HA / Glycerol metabolism
Function / homology
Function and homology information


phosphoenolpyruvate-glycerone phosphotransferase / phosphoenolpyruvate-glycerone phosphotransferase activity / glycerone kinase activity / glycerol catabolic process / cytosol
Similarity search - Function
Dihydroxyacetone kinase DhaK, subunit 1 / Dihydroxyacetone kinase; domain 2 / DhaK domain / Dak1 domain / DhaK domain profile. / : / Dihydroxyacetone kinase; domain 1 / Hypothetical Protein Tm841; Chain: A;domain 3 / Rossmann fold / 2-Layer Sandwich ...Dihydroxyacetone kinase DhaK, subunit 1 / Dihydroxyacetone kinase; domain 2 / DhaK domain / Dak1 domain / DhaK domain profile. / : / Dihydroxyacetone kinase; domain 1 / Hypothetical Protein Tm841; Chain: A;domain 3 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dihydroxyacetone / PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.498 Å
AuthorsJeckelmann, J.M. / Zurbriggen, A. / Christen, S. / Baumann, U. / Erni, B.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: X-ray Structures of the Three Lactococcus lactis Dihydroxyacetone Kinase Subunits and of a Transient Intersubunit Complex.
Authors: Zurbriggen, A. / Jeckelmann, J.M. / Christen, S. / Bieniossek, C. / Baumann, U. / Erni, B.
History
DepositionApr 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 8, 2013Group: Other
Revision 1.3Oct 25, 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
B: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
C: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1116
Polymers108,8413
Non-polymers2703
Water6,575365
1
A: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
hetero molecules

A: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7414
Polymers72,5612
Non-polymers1802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
MethodPISA
2
B: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
hetero molecules

B: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7414
Polymers72,5612
Non-polymers1802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_434x-y-1,-y-2,-z-1/31
MethodPISA
3
C: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
hetero molecules

C: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7414
Polymers72,5612
Non-polymers1802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
MethodPISA
4
A: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
hetero molecules

A: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
hetero molecules

B: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
C: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
hetero molecules

B: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
C: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,22312
Polymers217,6826
Non-polymers5406
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation4_545y,x-1,-z1
crystal symmetry operation3_544-x+y,-x-1,z-1/31
identity operation1_555x,y,z1
crystal symmetry operation5_434x-y-1,-y-2,-z-1/31
Buried area16510 Å2
ΔGint-107 kcal/mol
Surface area65840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.802, 107.802, 142.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUVALVALCHAIN A AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...AA4 - 1124 - 112
12ASNASNGLUGLUCHAIN A AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...AA114 - 116114 - 116
13ALAALAVALVALCHAIN A AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...AA118 - 140118 - 140
14THRTHRGLYGLYCHAIN A AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...AA146 - 148146 - 148
15ARGARGPROPROCHAIN A AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...AA150 - 199150 - 199
16ASPASPTRPTRPCHAIN A AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...AA210 - 331210 - 331
21GLUGLUVALVALCHAIN B AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...BB4 - 1124 - 112
22ASNASNGLUGLUCHAIN B AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...BB114 - 116114 - 116
23ALAALAVALVALCHAIN B AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...BB118 - 140118 - 140
24THRTHRGLYGLYCHAIN B AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...BB146 - 148146 - 148
25ARGARGPROPROCHAIN B AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...BB150 - 199150 - 199
26ASPASPTRPTRPCHAIN B AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...BB210 - 331210 - 331
31GLUGLUVALVALCHAIN C AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...CC4 - 1124 - 112
32ASNASNGLUGLUCHAIN C AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...CC114 - 116114 - 116
33ALAALAVALVALCHAIN C AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...CC118 - 140118 - 140
34THRTHRGLYGLYCHAIN C AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...CC146 - 148146 - 148
35ARGARGPROPROCHAIN C AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...CC150 - 199150 - 199
36ASPASPTRPTRPCHAIN C AND (RESSEQ 4:112 OR RESSEQ 114:116 OR RESSEQ...CC210 - 331210 - 331

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.998703, -0.046347, 0.021075), (-0.045524, -0.998241, -0.037983), (0.022798, 0.036975, -0.999056)-3.12291, -122.758003, -45.002701
3given(-0.603888, 0.797008, -0.009904), (-0.797052, -0.60391, 0.000936), (-0.005235, 0.00846, 0.999951)103.728996, -69.230698, -46.678398
DetailsThere are three monomers in the asymmetric unit. The biological assembly is a dimer. These three dimers are generated by the following operations: (i) Y,X,-Z (ii) X-Y,-Y,-Z +2/3 +(0 -1 -1) (iii) Y,X,-Z +(-1 -1 0)

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Components

#1: Protein PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK


Mass: 36280.406 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: lacI(q), oriR ColE1, kan, pT7, N-/C-term. hexahistidine tag
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Strain: IL 1403 / Gene: dhaK / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: Q9CIV8, Transferases; Transferring phosphorus-containing groups
#2: Sugar ChemComp-2HA / Dihydroxyacetone


Type: saccharide / Mass: 90.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsAUTHOR STATES THAT RESIDUE 59 (UNP NUMBERING) SHOULD BE GLU INSTEAD OF LYS

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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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.05 M TRIS/HCl, 0.2 M NH4Cl, 0.01 M CaCl2, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.79997 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 15, 2006
RadiationMonochromator: Double crystal Si[111], horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.79997 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. all: 36223 / Num. obs: 36223 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.09 / Χ2: 1.036 / Net I/σ(I): 9.4
Reflection shellResolution: 2.44→2.53 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.428 / Num. unique all: 2850 / Χ2: 0.922 / % possible all: 78

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UOD

1uod


Resolution: 2.498→44.372 Å / FOM work R set: 0.775 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1714 5.13 %Random
Rwork0.2 ---
all0.204 33435 --
obs0.2038 33435 98.69 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.644 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 4.72 Å2 / Biso mean: 38.86 Å2 / Biso min: 425.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.753 Å20 Å2-0 Å2
2---1.753 Å20 Å2
3----1.512 Å2
Refinement stepCycle: LAST / Resolution: 2.498→44.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 18 365 7703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067446
X-RAY DIFFRACTIONf_angle_d0.91310026
X-RAY DIFFRACTIONf_chiral_restr0.0661146
X-RAY DIFFRACTIONf_plane_restr0.0031290
X-RAY DIFFRACTIONf_dihedral_angle_d15.0692763
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2370X-RAY DIFFRACTIONPOSITIONAL0.028
12B2370X-RAY DIFFRACTIONPOSITIONAL0.028
13C2370X-RAY DIFFRACTIONPOSITIONAL0.033
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.498-2.5720.361460.2492416256291
2.572-2.6550.2941350.2426252760100
2.655-2.750.3521300.2382649277999
2.75-2.860.3851210.22426402761100
2.86-2.990.281450.2022647279299
2.99-3.1470.2731580.1962608276699
3.147-3.3450.2731480.1912633278199
3.345-3.6030.2461420.17626842826100
3.603-3.9650.2241600.1652636279699
3.965-4.5380.2071290.14927002829100
4.538-5.7160.221660.15827092875100
5.716-44.3790.2481340.2112774290897
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)
10.05250.0398-0.07290.48030.1039-0.01140.12420.1444-0.0361-0.1386-0.02850.0132-0.12980.0305-0.07790.2577-0.0288-0.010.1592-0.01060.084240.4426-39.8858-41.4583
20.90320.1881-0.21370.0296-0.16240.09480.0932-0.1256-0.14150.1379-0.0281-0.03660.08540.065-0.06830.25910.0174-0.00160.2445-0.01010.123336.284-49.6236-31.2914
30.8858-0.39940.16330.82420.05650.54420.0514-0.30720.03870.2440.03980.01050.17370.0664-0.06440.2182-0.0146-0.00540.1861-0.01050.053334.9133-44.9011-16.7447
40.8388-0.15260.63641.9846-0.22660.0893-0.1311-0.4310.00270.38440.26580.17090.10340.1068-0.08760.34280.04020.00770.2393-0.06550.157839.8203-84.6161-5.7783
51.8421-0.57161.09470.7072-0.61281.08510.0703-0.4360.0512-0.31790.12030.1141-0.3449-0.1219-0.1530.3188-0.0618-0.0150.1306-0.07230.310636.351-74.3117-15.6542
61.27910.0509-0.08991.0142-0.63890.82180.17910.08390.1772-0.05470.01750.337-0.24160.0874-0.16470.32330.006-0.04780.1334-0.0060.326235.0858-78.4375-30.3887
70.25810.31830.94820.33160.13370.6641-0.09560.3113-0.0332-0.27460.1289-0.0101-0.063-0.0475-0.02440.2042-0.05390.06070.27840.01710.088714.808-68.10985.8799
80.37380.22480.15390.6545-0.33521.3880.03440.12730.0262-0.1015-0.0563-0.1245-0.16550.21830.00520.1812-0.01040.01950.2833-0.00850.087124.9417-65.614716.0326
90.54730.13440.54631.3258-0.22460.9148-0.0134-0.0464-0.09380.1277-0.0379-0.0935-0.09230.15340.05930.1043-0.0150.03130.21860.03320.079922.0088-69.28830.639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND RESID 12:120A12 - 120
2X-RAY DIFFRACTION2CHAIN A AND RESID 121:220A121 - 220
3X-RAY DIFFRACTION3CHAIN A AND RESID 221:331A221 - 331
4X-RAY DIFFRACTION4CHAIN B AND RESID 12:120B12 - 120
5X-RAY DIFFRACTION5CHAIN B AND RESID 121:220B121 - 220
6X-RAY DIFFRACTION6CHAIN B AND RESID 221:331B221 - 331
7X-RAY DIFFRACTION7CHAIN C AND RESID 12:120C12 - 120
8X-RAY DIFFRACTION8CHAIN C AND RESID 121:220C121 - 220
9X-RAY DIFFRACTION9CHAIN C AND RESID 221:331C221 - 331

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