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

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Basic information

Entry
Database: PDB / ID: 4xfr
TitleCrystal structure of a domain of unknown function (DUF1537) from Bordetella bronchiseptica (BB3215), Target EFI-511620, with bound citrate, domain swapped dimer, space group P6522
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
CITRIC ACID / D-threonate kinase / D-threonate kinase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1826
Polymers87,4132
Non-polymers7684
Water8,593477
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0913
Polymers43,7071
Non-polymers3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0913
Polymers43,7071
Non-polymers3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-13 kcal/mol
Surface area30860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.637, 77.637, 479.012
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-619-

HOH

21B-646-

HOH

Detailsbiological unit is undetermined, could be monomer or dimer

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Components

#1: Protein Uncharacterized protein


Mass: 43706.688 Da / Num. of mol.: 2 / Fragment: DUF1537
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: ATCC BAA-588 / NCTC 13252 / RB50 / Gene: BB3215 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7WHJ2, UniProt: A0A0H3LX82*PLUS
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein (39.6 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT,); Reservoir (MCSG2(A9); 0.1 M tri-Sodium Citrate pH 5, 20 %(w/v) PEG 6000); 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: 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: 2→479.01 Å / Num. obs: 59286 / % possible obs: 99.2 % / Redundancy: 20.1 % / Biso Wilson estimate: 28.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.019 / Net I/σ(I): 24.1 / Num. measured all: 1194531 / Scaling rejects: 19
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.058.80.8072.63560640250.7180.24694
8.94-479.0129.30.04468.9259528850.9990.00899.5

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→36.55 Å / FOM work R set: 0.8398 / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 2982 5.05 %
Rwork0.1883 56083 -
obs0.1912 59065 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.31 Å2 / Biso mean: 35.18 Å2 / Biso min: 14.9 Å2
Refinement stepCycle: final / Resolution: 2→36.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5696 0 67 477 6240
Biso mean--36.33 36.39 -
Num. residues----802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135830
X-RAY DIFFRACTIONf_angle_d1.4087977
X-RAY DIFFRACTIONf_chiral_restr0.074958
X-RAY DIFFRACTIONf_plane_restr0.0071065
X-RAY DIFFRACTIONf_dihedral_angle_d16.8932031
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.03280.27871250.24392427255293
2.0328-2.06780.33651270.24652497262495
2.0678-2.10540.33971370.24412560269797
2.1054-2.14590.32141590.23732537269698
2.1459-2.18970.28281370.23732588272599
2.1897-2.23730.33251580.228326332791100
2.2373-2.28940.33661240.237126622786100
2.2894-2.34660.27311350.199826472782100
2.3466-2.41010.2421300.194326532783100
2.4101-2.4810.24441240.183226582782100
2.481-2.5610.27041470.185426552802100
2.561-2.65250.24621520.198526602812100
2.6525-2.75870.28161280.194626992827100
2.7587-2.88420.23871440.199526812825100
2.8842-3.03620.2791490.197626632812100
3.0362-3.22630.24841420.194427442886100
3.2263-3.47520.2321380.182227042842100
3.4752-3.82460.23921370.170827622899100
3.8246-4.37730.21331700.157927622932100
4.3773-5.51190.17971430.151228382981100
5.5119-36.55630.20141760.184230533229100
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)
12.9136-0.4195-0.37553.7687-0.28361.84660.00990.57030.1066-0.5275-0.0112-0.41320.25680.0426-0.03140.26610.02080.04130.3797-0.03470.248751.095446.171113.7751
23.96040.201-1.4891.4171-0.01633.6908-0.21860.3344-0.15560.03960.00820.07220.424-0.40320.1080.2244-0.03160.02080.2081-0.05880.222137.492942.244525.3675
31.0257-1.8426-0.64455.68581.1790.4055-0.0645-0.00080.091-0.06620.0672-0.1207-0.1505-0.1076-0.0260.3025-0.0070.01510.3067-0.03230.265151.195522.005417.3007
41.28181.5879-0.02263.1137-0.05011.3899-0.0405-0.0066-0.03270.06440.06070.10230.0608-0.0199-0.02040.17040.0676-0.00380.2572-0.04550.222257.06138.678413.6408
51.60830.09830.21052.0075-0.40371.69740.09450.2151-0.2079-0.1929-0.0187-0.08950.24330.1682-0.05770.2110.0537-0.01850.2613-0.06340.213480.579120.548917.9602
62.1490.58830.89122.0380.32082.41940.1141-0.1576-0.04410.2855-0.1003-0.05230.0961-0.1173-0.00990.22750.0217-0.01710.2252-0.04210.176884.965727.378332.1681
72.8110.4017-0.26241.933-0.20242.20890.1725-0.36810.5170.2454-0.39110.2157-0.1566-0.12230.14780.2464-0.01740.05930.3785-0.14080.410372.200464.146122.5529
82.73050.98370.8453.1945-0.02541.33240.0618-0.26460.3424-0.142-0.15310.1429-0.1062-0.01930.07260.15720.03550.03860.2497-0.05210.248665.953552.558216.8217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 62 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 216 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 245 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 246 through 404 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 124 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 125 through 232 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 233 through 309 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 310 through 404 )B0

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