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- PDB-4xg0: Crystal structure of a domain of unknown function (DUF1537) from ... -

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Basic information

Entry
Database: PDB / ID: 4xg0
TitleCrystal structure of a domain of unknown function (DUF1537) from Bordetella bronchiseptica (BB3215), Target EFI-511620, with bound citrate, domain swapped dimer, space group C2221
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.0Mar 11, 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
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)44,0356
Polymers43,5191
Non-polymers5165
Water4,792266
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)88,07012
Polymers87,0382
Non-polymers1,03210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4800 Å2
ΔGint-81 kcal/mol
Surface area29680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.064, 92.903, 133.157
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Detailsbiological unit is undetermined, could be monomer or dimer

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Components

#1: Protein Uncharacterized protein


Mass: 43519.105 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
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(H6); 0.8 M Ammonium Sulfate, 0.1 M tri-Sodium Citrate, pH 4); Cryoprotection (80% 1.8 M LiSO4, 20% Reservoir

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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: 1.7→32.09 Å / Num. obs: 43285 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 25.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.038 / Net I/σ(I): 10 / Num. measured all: 318618 / Scaling rejects: 185
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
1.7-1.737.30.9042.11656022550.7530.358100
9-32.095.20.07617.313662630.9920.03376.8

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Processing

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

4xfr


Resolution: 1.7→30.683 Å / FOM work R set: 0.8246 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2365 2172 5.03 %
Rwork0.1987 41012 -
obs0.2006 43184 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.19 Å2 / Biso mean: 34.26 Å2 / Biso min: 14.03 Å2
Refinement stepCycle: final / Resolution: 1.7→30.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 34 266 3079
Biso mean--42.33 37.34 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112878
X-RAY DIFFRACTIONf_angle_d1.3053945
X-RAY DIFFRACTIONf_chiral_restr0.077474
X-RAY DIFFRACTIONf_plane_restr0.008526
X-RAY DIFFRACTIONf_dihedral_angle_d15.349996
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.7370.29321220.258625082630100
1.737-1.77740.2781250.240125552680100
1.7774-1.82180.251460.232125442690100
1.8218-1.87110.29821610.227925192680100
1.8711-1.92610.3291220.259425332655100
1.9261-1.98830.24861400.219725422682100
1.9883-2.05930.29441310.208825482679100
2.0593-2.14180.23681350.200925552690100
2.1418-2.23920.2351320.200825762708100
2.2392-2.35720.21951420.194325332675100
2.3572-2.50490.23631300.183325702700100
2.5049-2.69820.23831350.196725832718100
2.6982-2.96950.24411270.208125962723100
2.9695-3.39870.25311410.207625902731100
3.3987-4.28010.20571470.172126232770100
4.2801-30.68830.21721360.19142637277397
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)
10.683-0.4162-0.77721.43260.73252.3668-0.40910.5803-0.5512-0.08790.07460.23920.7855-0.75660.24960.3916-0.15260.10260.3978-0.12640.26285.4256-4.7873-16.2684
23.55370.5581-1.96671.8201-0.06633.266-0.21640.66440.139-0.37630.2047-0.2380.0596-0.355-0.07560.278-0.05240.07980.2451-0.02560.117317.98664.1613-24.4354
32.16390.0049-0.13751.79880.65531.4732-0.0077-0.12830.40080.0505-0.015-0.1441-0.04570.03320.02980.14180.0072-0.01010.1714-0.06920.27978.042423.87416.6142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 62 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 232 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 233 through 404 )A0

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