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- PDB-4ebu: Crystal structure of a sugar kinase (Target EFI-502312) from Ocea... -

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Basic information

Entry
Database: PDB / ID: 4ebu
TitleCrystal structure of a sugar kinase (Target EFI-502312) from Oceanicola granulosus, with bound AMP/ADP crystal form I
Components2-dehydro-3-deoxygluconokinase
KeywordsTRANSFERASE / putative sugar kinase / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


D-galacturonate catabolic process / 2-dehydro-3-deoxygluconokinase activity / D-glucuronate catabolic process / DNA damage response / metal ion binding / cytosol
Similarity search - Function
pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / KDG kinase
Similarity search - Component
Biological speciesOceanicola granulosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a sugar kinase (Target EFI-502312) from Oceanicola granulosus, with bound AMP/ADP crystal form I
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionMar 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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 / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-dehydro-3-deoxygluconokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4234
Polymers34,6131
Non-polymers8103
Water4,450247
1
A: 2-dehydro-3-deoxygluconokinase
hetero molecules

A: 2-dehydro-3-deoxygluconokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8468
Polymers69,2262
Non-polymers1,6206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+5/31
Buried area4860 Å2
ΔGint-44 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.308, 94.308, 82.959
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-652-

HOH

21A-669-

HOH

31A-672-

HOH

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Components

#1: Protein 2-dehydro-3-deoxygluconokinase / sugar kinase


Mass: 34612.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oceanicola granulosus (bacteria) / Strain: HTCC2516 / Gene: OG2516_05533 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2CIP5, 2-dehydro-3-deoxygluconokinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: 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
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: protein (10 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 1 mM DTT, 5 mM AMP-PNP), reservoir (0.1 M sodium acetate, pH 4.6, 1.5 M ammonium chloride), cryoprotection (reservoir + ...Details: protein (10 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 1 mM DTT, 5 mM AMP-PNP), reservoir (0.1 M sodium acetate, pH 4.6, 1.5 M ammonium chloride), cryoprotection (reservoir + 20% glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: Feb 19, 2012 / Details: mirrors
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→82.959 Å / Num. all: 29081 / Num. obs: 29081 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.115.40.6651.12291842090.665100
2.11-2.245.50.4651.52187740090.465100
2.24-2.395.50.3252.22034137260.325100
2.39-2.585.50.2133.41925835250.213100
2.58-2.835.50.1394.91765132280.139100
2.83-3.165.50.0946.91608129470.094100
3.16-3.655.40.0916.21415025980.091100
3.65-4.475.40.0926.41207722360.092100
4.47-6.325.30.0649.3919517370.06499.8
6.32-36.6384.70.04315.140438660.04385.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
MAR345data collection
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E69

4e69


Resolution: 2→36.638 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.8486 / SU ML: 0.23 / σ(F): 0 / σ(I): 0 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 1473 5.08 %RANDOM
Rwork0.1772 ---
all0.179 29018 --
obs0.179 29018 99.36 %-
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.023 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 107.42 Å2 / Biso mean: 39.7392 Å2 / Biso min: 18.72 Å2
Baniso -1Baniso -2Baniso -3
1-8.2559 Å2-0 Å2-0 Å2
2--8.2559 Å20 Å2
3----16.5117 Å2
Refinement stepCycle: LAST / Resolution: 2→36.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 51 247 2553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072375
X-RAY DIFFRACTIONf_angle_d1.0943240
X-RAY DIFFRACTIONf_chiral_restr0.072364
X-RAY DIFFRACTIONf_plane_restr0.004422
X-RAY DIFFRACTIONf_dihedral_angle_d15.172841
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.06460.34321330.280724862619100
2.0646-2.13830.24971430.234824712614100
2.1383-2.2240.26811370.217224412578100
2.224-2.32520.27231140.199625332647100
2.3252-2.44770.23131310.18724972628100
2.4477-2.6010.2191360.179124942630100
2.601-2.80180.18661320.166325172649100
2.8018-3.08360.22741410.175625042645100
3.0836-3.52950.22091480.177225222670100
3.5295-4.44560.19141440.146725432687100
4.4456-36.64430.17891140.17062537265195
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)
10.83080.2420.34690.2225-0.04175.6473-0.060.06160.0222-0.04890.03720.0367-0.2399-0.35340.03110.25340.04560.00580.17810.02580.239680.636183.530485.3555
22.3936-0.7282-0.48582.906-0.50263.20220.09580.1186-0.0782-0.2026-0.1183-0.19860.16810.3061-0.00860.10940.0242-0.00060.17020.00580.191195.122974.14290.1431
32.3530.1759-0.40793.6658-0.10792.70270.02360.0909-0.2545-0.03370.05260.07720.5084-0.2652-0.090.3136-0.0469-0.03690.174-0.00570.207381.832763.694595.7902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq -13:108)A-13 - 108
2X-RAY DIFFRACTION2chain 'A' and (resseq 109:204)A109 - 204
3X-RAY DIFFRACTION3chain 'A' and (resseq 205:296)A205 - 296

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