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- PDB-4e69: Crystal structure of a sugar kinase (target EFI-502132) from Ocea... -

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Basic information

Entry
Database: PDB / ID: 4.0E+69
TitleCrystal structure of a sugar kinase (target EFI-502132) from Oceanicola granulosus, unliganded structure
Components2-dehydro-3-deoxygluconokinase
KeywordsTRANSFERASE / putative sugar kinase / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


organic substance metabolic process / kinase activity / phosphorylation / nucleotide binding
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
Biological speciesOceanicola granulosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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-502132) from Oceanicola granulosus, unliganded structure
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 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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
B: 2-dehydro-3-deoxygluconokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,80913
Polymers69,2262
Non-polymers58311
Water12,106672
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-70 kcal/mol
Surface area26000 Å2
MethodPISA
2
A: 2-dehydro-3-deoxygluconokinase
hetero molecules

B: 2-dehydro-3-deoxygluconokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,80913
Polymers69,2262
Non-polymers58311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area3480 Å2
ΔGint-78 kcal/mol
Surface area25940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.249, 76.306, 76.245
Angle α, β, γ (deg.)90.000, 105.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34612.984 Da / Num. of mol.: 2
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: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: Protein (10 mM HEPES pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT; Reservoir (1 M LiCl, 0.1 M NaCitrate pH 4, 20% Peg 6000); Cryoprotection (Reservoir, + 20% Ethyelene Glycol), VAPOR ...Details: Protein (10 mM HEPES pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT; Reservoir (1 M LiCl, 0.1 M NaCitrate pH 4, 20% Peg 6000); Cryoprotection (Reservoir, + 20% Ethyelene Glycol), 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: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 84535 / Num. obs: 84535 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 19.51 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 9
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 1.6 / Num. unique all: 12335 / Rsym value: 0.837 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LHX

3lhx


Resolution: 1.6→28.024 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.8819 / SU ML: 0.22 / σ(F): 0 / σ(I): 0 / Phase error: 19.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1968 4212 4.99 %RANDOM
Rwork0.1678 ---
all0.1693 84483 --
obs0.1693 84483 99.76 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.886 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso max: 84.74 Å2 / Biso mean: 25.4174 Å2 / Biso min: 8.49 Å2
Baniso -1Baniso -2Baniso -3
1-3.066 Å2-0 Å2-1.753 Å2
2--2.949 Å2-0 Å2
3----6.015 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4579 0 30 672 5281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064954
X-RAY DIFFRACTIONf_angle_d1.0046755
X-RAY DIFFRACTIONf_chiral_restr0.072743
X-RAY DIFFRACTIONf_plane_restr0.004918
X-RAY DIFFRACTIONf_dihedral_angle_d12.881801
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61820.34051420.317127092851100
1.6182-1.63720.34831370.308126442781100
1.6372-1.65720.32151440.306727122856100
1.6572-1.67820.33281400.290526252765100
1.6782-1.70020.31871350.258826832818100
1.7002-1.72350.27791410.249226572798100
1.7235-1.74810.26461390.240926682807100
1.7481-1.77420.27031240.225827292853100
1.7742-1.8020.25231320.206226272759100
1.802-1.83150.23181390.187726972836100
1.8315-1.86310.21671620.178426172779100
1.8631-1.89690.20891400.172726692809100
1.8969-1.93340.19291420.168426652807100
1.9334-1.97290.20471460.16226472793100
1.9729-2.01580.20581340.164526862820100
2.0158-2.06260.19761160.156327002816100
2.0626-2.11420.16581390.16126862825100
2.1142-2.17130.18451420.157626622804100
2.1713-2.23520.19651470.155926752822100
2.2352-2.30730.17891450.148926682813100
2.3073-2.38970.19841680.152626642832100
2.3897-2.48540.20061340.157826542788100
2.4854-2.59840.21571140.156227282842100
2.5984-2.73530.18751630.156326722835100
2.7353-2.90650.181470.159427042851100
2.9065-3.13060.18521420.163726542796100
3.1306-3.44520.17051250.153627252850100
3.4452-3.94250.15831450.141826952840100
3.9425-4.96270.16531470.135427092856100
4.9627-28.02820.20541410.18742640278195
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)
11.1234-0.19390.68380.71510.11161.92150.058-0.1153-0.06250.0027-0.05650.03750.1456-0.18030.01040.0713-0.01680.00490.08720.00290.11298.828848.3347.3497
21.7032-0.2280.49791.2045-0.60920.96670.0220.0110.05820.0081-0.0426-0.04590.01590.05570.02350.1214-0.00130.00770.085-0.01790.127524.896759.68147.0143
31.0810.22980.49880.97780.3151.61230.0457-0.002-0.19820.12360.0176-0.17180.17390.0881-0.05780.13830.0223-0.01180.1020.00530.1828.177942.081548.9254
40.1199-0.08690.3390.0335-0.33771.43540.04120.0603-0.0681-0.06590.04260.01170.227-0.1168-0.07290.20320.0061-0.0180.1830.00430.1736-5.135846.035410.9454
51.0298-0.30950.7050.9349-0.15872.5471-0.01320.0790.0072-0.0147-0.0024-0.0770.03650.07280.01610.11470.00640.01520.12080.00410.1417-2.990550.387719.2855
62.167-0.5686-0.4961.13830.33611.1517-0.0434-0.00810.240.05260.0001-0.0788-0.2084-0.07690.06080.18570.02610.00210.13430.01250.1633-13.452964.054118.4305
72.2756-0.37210.10511.62940.82511.73050.05790.0044-0.22560.1328-0.12130.24980.1137-0.4050.04250.1435-0.02380.02290.2725-0.00430.1523-24.733151.370617.3802
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 109:233)A109 - 233
3X-RAY DIFFRACTION3chain 'A' and (resseq 234:296)A234 - 296
4X-RAY DIFFRACTION4chain 'B' and (resseq -13:21)B-13 - 21
5X-RAY DIFFRACTION5chain 'B' and (resseq 22:137)B22 - 137
6X-RAY DIFFRACTION6chain 'B' and (resseq 138:204)B138 - 204
7X-RAY DIFFRACTION7chain 'B' and (resseq 205:297)B205 - 297

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