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

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Basic information

Entry
Database: PDB / ID: 4xgj
TitleCrystal structure of a domain of unknown function (DUF1537) from Pectobacterium atrosepticum (ECA3761), Target EFI-511609, APO structure, 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
Biological speciesPectobacterium atrosepticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Aug 10, 2016Group: Database references
Revision 1.4Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)49,5601
Polymers49,5601
Non-polymers00
Water6,017334
1


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

A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)99,1202
Polymers99,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3010 Å2
ΔGint-26 kcal/mol
Surface area32580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.772, 47.844, 63.792
Angle α, β, γ (deg.)90.00, 106.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-593-

HOH

Detailsbiological unit is undetermined, could be monomer or dimer

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Components

#1: Protein Uncharacterized protein


Mass: 49559.852 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 45.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (46.8 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (MCSG4 (F4); 0.2 M Magnesium Chloride, 0.1 M Tris pH 8.5, 16 %(w/v) PEG 4000); Cryoprotection (80% Reservoir, 20% glycerol)

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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: Jun 12, 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: 1.9→73.65 Å / Num. obs: 35312 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→41.53 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 1763 5 %
Rwork0.156 --
obs0.158 35287 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.77 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 0 334 3277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112996
X-RAY DIFFRACTIONf_angle_d1.2954081
X-RAY DIFFRACTIONf_dihedral_angle_d13.7411062
X-RAY DIFFRACTIONf_chiral_restr0.073505
X-RAY DIFFRACTIONf_plane_restr0.006531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95140.27871480.2172557X-RAY DIFFRACTION100
1.9514-2.00880.25691260.19342566X-RAY DIFFRACTION100
2.0088-2.07370.20161340.16772550X-RAY DIFFRACTION100
2.0737-2.14780.22581110.15612600X-RAY DIFFRACTION100
2.1478-2.23380.17691160.15212577X-RAY DIFFRACTION100
2.2338-2.33540.19141360.14912551X-RAY DIFFRACTION100
2.3354-2.45850.18221280.14682592X-RAY DIFFRACTION100
2.4585-2.61260.20081300.15052576X-RAY DIFFRACTION100
2.6126-2.81420.19531600.15292557X-RAY DIFFRACTION100
2.8142-3.09740.21811440.15422590X-RAY DIFFRACTION100
3.0974-3.54530.17731420.15122580X-RAY DIFFRACTION100
3.5453-4.46590.15971500.13942602X-RAY DIFFRACTION100
4.4659-41.54110.19521380.16872626X-RAY DIFFRACTION98
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)
11.72341.02490.15922.7810.22261.81550.0165-0.07180.1774-0.08020.00020.1372-0.1510.0496-0.0190.1063-0.0032-0.00660.1140.01630.156152.369317.63365.7507
23.04180.5710.65524.4484-0.00052.3884-0.08870.0051-0.2013-0.21770.0868-0.27040.07460.09660.00550.10680.00640.02290.1102-0.01190.111356.16551.11430.1164
31.54930.30970.18773.18620.38834.2221-0.08190.5323-0.2295-0.57240.0882-0.5117-0.06230.52110.04450.301-0.01950.08220.3811-0.06820.253886.00620.913828.8643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 9 THROUGH 110 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 111 THROUGH 238 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 239 THROUGH 439 )

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