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- PDB-3ct6: Crystal structure of DhaM of L. lactis -

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Basic information

Entry
Database: PDB / ID: 3ct6
TitleCrystal structure of DhaM of L. lactis
ComponentsPTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM
KeywordsTRANSFERASE / mixed alpha beta structure / Glycerol metabolism / Kinase / Phosphotransferase system
Function / homology
Function and homology information


phosphoenolpyruvate-glycerone phosphotransferase / phosphoenolpyruvate-glycerone phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / glycerol catabolic process / phosphorylation / ATP binding / membrane
Similarity search - Function
Dihydroxyacetone kinase phosphotransferase subunit, N-terminal domain / Dihydroxyacetone kinase phosphotransferase subunit DhaM / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit DhaM
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / SAD / Resolution: 1.1 Å
AuthorsZurbriggen, A.
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 1.2Aug 23, 2017Group: Advisory / Data collection / Source and taxonomy
Category: diffrn_detector / entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_detector.detector / _diffrn_detector.type ..._diffrn_detector.detector / _diffrn_detector.type / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.3Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM
B: PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM


Theoretical massNumber of molelcules
Total (without water)28,9572
Polymers28,9572
Non-polymers00
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-16.5 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.600, 62.400, 69.700
Angle α, β, γ (deg.)90.00, 99.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM / Phosphotransferase enzyme IIA component / PTS system EIIA component


Mass: 14478.470 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: dhaM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9CIV6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 289 K / pH: 2.8
Details: 200 mM NaNO3, 20 % PEG 3350, pH 2.8, 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
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.79997 Å / Relative weight: 1
ReflectionResolution: 1.1→40 Å / Num. obs: 97245 / % possible obs: 93 % / Redundancy: 2.489 % / Biso Wilson estimate: 12.936 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 17.41
Reflection shellResolution: 1.1→1.136 Å / Redundancy: 2.218 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 4.4 / % possible all: 90.77

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Os35.6620.5660.8760.0470.369
2Os34.8950.5840.8910.4670.36
3Os48.8250.9040.690.3580.203

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLVE2.08phasing
RESOLVE2.08phasing
SHELXrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
SHELXphasing
SHELXL-97refinement
RefinementMethod to determine structure: AB INITIO / Resolution: 1.1→40 Å / Num. parameters: 20985 / Num. restraintsaints: 26479 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1769 1987 2 %RANDOM
all0.1462 97245 --
obs0.1468 -93 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 17.891 Å2
Refine analyzeNum. disordered residues: 15 / Occupancy sum hydrogen: 1943.92 / Occupancy sum non hydrogen: 2190.46
Refinement stepCycle: LAST / Resolution: 1.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4201 0 0 255 4456
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0275
X-RAY DIFFRACTIONs_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.147
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.051
X-RAY DIFFRACTIONs_approx_iso_adps0.065

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