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- PDB-4xfm: Crystal structure of a domain of unknown function (DUF1537) from ... -

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Basic information

Entry
Database: PDB / ID: 4xfm
TitleCrystal structure of a domain of unknown function (DUF1537) from Pectobacterium atrosepticum (ECA3761), Target EFI-511609, with bound D-threonate, domain swapped dimer
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / ENZYME FUNCTION INITIATIVE / EFI
Function / homology
Function and homology information


D-threonate 4-kinase / kinase activity / carbohydrate metabolic process / phosphorylation / ATP binding
Similarity search - Function
Four-carbon acid sugar kinase, N-terminal domain / Four-carbon acid sugar kinase, nucleotide binding domain / Four-carbon acid sugar kinase, N-terminal domain superfamily / Four-carbon acid sugar kinase, nucleotide binding domain superfamily / Sugar-binding N-terminal domain / Nucleotide-binding C-terminal domain
Similarity search - Domain/homology
THREONATE ION / D-threonate kinase
Similarity search - Component
Biological speciesPectobacterium atrosepticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. ...Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars.
Authors: Zhang, X. / Carter, M.S. / Vetting, M.W. / San Francisco, B. / Zhao, S. / Al-Obaidi, N.F. / Solbiati, J.O. / Thiaville, J.J. / de Crecy-Lagard, V. / Jacobson, M.P. / Almo, S.C. / Gerlt, J.A.
History
DepositionDec 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Data collection
Revision 1.2Jul 13, 2016Group: Database references
Revision 1.3Jul 27, 2016Group: Database references
Revision 1.4Aug 10, 2016Group: Database references
Revision 1.5Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4142
Polymers49,2781
Non-polymers1351
Water7,314406
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8274
Polymers98,5572
Non-polymers2702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3690 Å2
ΔGint-23 kcal/mol
Surface area32180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.696, 47.611, 64.142
Angle α, β, γ (deg.)90.000, 107.120, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is undetermined, could be monomer or dimer

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Components

#1: Protein Uncharacterized protein


Mass: 49278.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum (bacteria) / Strain: SCRI 1043 / ATCC BAA-672 / Gene: ECA3761 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6D0N7
#2: Chemical ChemComp-THE / THREONATE ION / Threonic acid


Mass: 135.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein (67.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-Threonate); Reservoir (MCSG1(F1); 0.1 M Bis-Tris pH 6.5, 20%(w/v) PEG MME 5000); Cryoprotection (80% Reservoir, 20% ethylene glycol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 10, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.55→61.3 Å / Num. obs: 63987 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.92 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.03 / Net I/σ(I): 14 / Num. measured all: 234457 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.55-1.583.70.6592.21166431670.7160.39899.1
8.49-61.32.80.03429.47372660.9840.02460.9

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XGJ

4xgj


Resolution: 1.55→27.919 Å / FOM work R set: 0.8859 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1909 3247 5.08 %
Rwork0.1645 60726 -
obs0.1658 63973 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.48 Å2 / Biso mean: 30.56 Å2 / Biso min: 10.8 Å2
Refinement stepCycle: final / Resolution: 1.55→27.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2947 0 9 409 3365
Biso mean--14.66 38.79 -
Num. residues----401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013000
X-RAY DIFFRACTIONf_angle_d1.2694087
X-RAY DIFFRACTIONf_chiral_restr0.071507
X-RAY DIFFRACTIONf_plane_restr0.007532
X-RAY DIFFRACTIONf_dihedral_angle_d12.7721068
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.57320.27511360.24052650278699
1.5732-1.59770.2641300.23432639276998
1.5977-1.62390.26961390.2172592273199
1.6239-1.65190.26131320.21042637276998
1.6519-1.6820.221390.197826232762100
1.682-1.71430.26761340.1952643277799
1.7143-1.74930.24481400.187826412781100
1.7493-1.78730.22111460.18032641278799
1.7873-1.82890.18691380.16512640277899
1.8289-1.87460.19131320.170526192751100
1.8746-1.92530.20591640.1722599276399
1.9253-1.98190.17711460.163226662812100
1.9819-2.04590.17361370.161426502787100
2.0459-2.1190.17181490.15812603275299
2.119-2.20380.20861510.158126512802100
2.2038-2.30410.20691180.15362672279099
2.3041-2.42550.18871510.145326532804100
2.4255-2.57730.19751790.152126512830100
2.5773-2.77620.17981330.15626772810100
2.7762-3.05520.19631530.152626482801100
3.0552-3.49660.16591440.159526812825100
3.4966-4.40260.16551360.14962696283299
4.4026-27.92330.19551200.1812554267491
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)
11.84970.3219-0.05912.73870.15071.4014-0.03210.0513-0.0648-0.14280.05120.019-0.01590.0967-0.0190.0901-0.0109-0.00650.11420.02290.092654.46198.23962.5311
20.92740.0421-0.18441.94920.40432.1888-0.17650.4331-0.067-0.43650.108-0.19360.0840.17090.06130.3208-0.06350.03950.3175-0.03510.177885.730920.862128.9056
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 238 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 239 through 439 )A0

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