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- PDB-5dmh: Crystal structure of a domain of unknown function (DUF1537) from ... -

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Basic information

Entry
Database: PDB / ID: 5dmh
TitleCrystal structure of a domain of unknown function (DUF1537) from Ralstonia eutropha H16 (H16_A1561), Target EFI-511666, complex with ADP.
ComponentsUncharacterized protein conserved in bacteria
KeywordsUNKNOWN FUNCTION / DOMAIN OF UNKNOWN FUNCTION / DUF1537 / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


3-dehydrotetronate 4-kinase / kinase activity / carbohydrate metabolic process / ATP binding
Similarity search - Function
Putative sugar-binding, N-terminal domain / Four-carbon acid sugar kinase, nucleotide binding domain / 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 / Molybdenum Cofactor Biosythetic Enzyme; Chain A / Rossmann fold ...Putative sugar-binding, N-terminal domain / Four-carbon acid sugar kinase, nucleotide binding domain / 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 / Molybdenum Cofactor Biosythetic Enzyme; Chain A / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 3-oxo-tetronate kinase
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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: To be published
Title: Crystal structure of a domain of unknown function (DUF1537) from Ralstonia eutropha H16 (H16_A1561), Target EFI-511666, complex with ADP.
Authors: Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Chamala, S. / Chowdhury, S. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S. ...Authors: Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Chamala, S. / Chowdhury, S. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionSep 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein conserved in bacteria
B: Uncharacterized protein conserved in bacteria
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2613
Polymers94,8342
Non-polymers4271
Water14,574809
1
A: Uncharacterized protein conserved in bacteria
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8442
Polymers47,4171
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein conserved in bacteria


Theoretical massNumber of molelcules
Total (without water)47,4171
Polymers47,4171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.130, 87.666, 178.988
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein conserved in bacteria


Mass: 47416.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (bacteria)
Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: H16_A1561 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0KBC8
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (30 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM ATP, 5 mM MgCl2); Reservoir (MCSG1 (H1) - 0.2 M Ammonium Fluoride, 20%(w/v) PEG 3350); 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: Nov 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: 1.8→39.365 Å / Num. obs: 78487 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 22.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.029 / Net I/σ(I): 17.3 / Num. measured all: 996969 / Scaling rejects: 26
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
1.8-1.8410.80.8572.74804644590.8520.271100
9.18-178.9910.90.0563975436890.9970.01897.5

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.8→39.365 Å / FOM work R set: 0.888 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1853 3943 5.03 %
Rwork0.1529 74421 -
obs0.1546 78364 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94 Å2 / Biso mean: 27.53 Å2 / Biso min: 9.98 Å2
Refinement stepCycle: final / Resolution: 1.8→39.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6077 0 39 809 6925
Biso mean--18.19 35.17 -
Num. residues----836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016218
X-RAY DIFFRACTIONf_angle_d1.2828466
X-RAY DIFFRACTIONf_chiral_restr0.073995
X-RAY DIFFRACTIONf_plane_restr0.0071130
X-RAY DIFFRACTIONf_dihedral_angle_d14.3222228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8220.24051210.214826432764100
1.822-1.8450.251500.207326022752100
1.845-1.86930.23661460.191226252771100
1.8693-1.89490.21671270.183526642791100
1.8949-1.9220.23641310.182425762707100
1.922-1.95070.2261260.176826592785100
1.9507-1.98120.21971470.168726322779100
1.9812-2.01360.21491290.161726412770100
2.0136-2.04840.17161450.157126362781100
2.0484-2.08560.21241210.159726242745100
2.0856-2.12570.22371370.155426652802100
2.1257-2.16910.21981330.154226042737100
2.1691-2.21630.19461420.152426732815100
2.2163-2.26780.20941370.14826112748100
2.2678-2.32450.1951490.144426542803100
2.3245-2.38740.20371520.135726222774100
2.3874-2.45760.16511470.135326432790100
2.4576-2.53690.17921630.13626152778100
2.5369-2.62760.17031420.136926592801100
2.6276-2.73270.18731460.141126332779100
2.7327-2.85710.17271480.143426772825100
2.8571-3.00770.19321400.147826762816100
3.0077-3.1960.17771320.154326882820100
3.196-3.44260.18191390.150826792818100
3.4426-3.78880.17291470.147327142861100
3.7888-4.33650.16411400.133427092849100
4.3365-5.46120.14811310.139427712902100
5.4612-39.37430.18321750.1922826300199
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)
10.98340.1661-0.74911.43060.02231.35190.03590.10720.2194-0.1189-0.03360.2982-0.0872-0.3960.00550.12980.0287-0.03870.25280.00370.26769.265188.0113119.185
20.12790.14260.05190.9992-0.38331.43990.0199-0.01370.04450.0316-0.0248-0.0056-0.1209-0.01910.00610.1133-0.0007-0.01070.1427-0.00440.177921.985590.6217132.5322
30.6963-0.3324-0.20251.74750.50991.32380.04950.0788-0.0133-0.1707-0.1210.14920.1055-0.20860.04460.1167-0.0117-0.02520.17330.00150.146315.971771.4334115.8217
41.0144-0.09270.58511.301-0.25711.29420.08640.0605-0.1235-0.4076-0.05160.10350.05170.0095-0.02760.2380.029-0.03390.1264-0.01280.155621.22429.5185106.3709
51.0049-0.55680.70390.7571-0.44940.4939-0.1103-0.03970.17630.04740.0403-0.0350.0145-0.02170.08360.265-0.00630.00440.19750.00510.10875.407549.804893.2693
61.88820.0607-0.99370.98340.0122.07410.0872-0.3707-0.04840.2734-0.02930.3146-0.13170.14620.00120.3677-0.02490.0240.28610.02310.2616-10.325345.716698.415
71.5633-0.25410.39141.14720.19661.2070.03120.15990.0121-0.1297-0.0176-0.05440.19830.0775-0.00880.35240.0295-0.03470.22190.01310.16167.987547.334590.1809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 67 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 232 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 233 through 430 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 232 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 233 through 327 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 328 through 361 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 362 through 432 )B0

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