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- PDB-4eun: Crystal structure of a sugar kinase (Target EFI-502144 from Janib... -

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Basic information

Entry
Database: PDB / ID: 4eun
TitleCrystal structure of a sugar kinase (Target EFI-502144 from Janibacter sp. HTCC2649), unliganded structure
Componentsthermoresistant glucokinase
KeywordsTRANSFERASE / putative sugar kinase / Enzyme Function Initiative / EFI / Structural Genomics
Function / homology
Function and homology information


gluconokinase / gluconokinase activity / carbohydrate metabolic process / ATP binding
Similarity search - Function
Carbohydrate kinase, thermoresistant glucokinase / Shikimate kinase/gluconokinase / Shikimate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesJanibacter sp. HTCC2649 (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-502144 from Janibacter sp. HTCC2649), 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
DepositionApr 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 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: thermoresistant glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2673
Polymers22,0751
Non-polymers1922
Water2,396133
1
A: thermoresistant glucokinase
hetero molecules

A: thermoresistant glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5346
Polymers44,1502
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area3990 Å2
ΔGint-82 kcal/mol
Surface area14330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.088, 51.088, 119.616
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-202-

SO4

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Components

#1: Protein thermoresistant glucokinase / Carbohydrate kinase


Mass: 22074.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Janibacter sp. HTCC2649 (bacteria) / Strain: HTCC2649 / Gene: JNB_15458 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3TPB6, gluconokinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 298 K / Method: sitting drop, vapor diffusion / pH: 7
Details: protein (10 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 1 mM DTT), reservoir (0.1 M Bis-Tris propane, pH 7.0, 2.5 M ammonium sulfate), cryoprotection (reservoir + 20% glycerol), ...Details: protein (10 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 1 mM DTT), reservoir (0.1 M Bis-Tris propane, pH 7.0, 2.5 M ammonium sulfate), cryoprotection (reservoir + 20% glycerol), SITTING DROP, VAPOR DIFFUSION, 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: 1.6→44.244 Å / Num. all: 24591 / Num. obs: 24591 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rsym value: 0.065 / Net I/σ(I): 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.6910.30.76213643135270.762100
1.69-1.7910.50.5161.53498633340.516100
1.79-1.9110.70.2622.93367031610.262100
1.91-2.0710.70.14953147429520.149100
2.07-2.2610.60.0937.62889127180.093100
2.26-2.5310.60.0719.52645624950.071100
2.53-2.9210.50.05710.72306721990.057100
2.92-3.5810.40.04612.51953618870.046100
3.58-5.069.50.042141403714810.04298.5
5.06-119.6168.20.0414.968278370.0493.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
MAR345data collection
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3T61

3t61


Resolution: 1.6→35.569 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8424 / SU ML: 0.16 / σ(F): 1.34 / Phase error: 22.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 1252 5.1 %RANDOM
Rwork0.1853 ---
obs0.1872 24531 99.59 %-
all-24531 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.428 Å2 / ksol: 0.407 e/Å3
Displacement parametersBiso max: 113.32 Å2 / Biso mean: 33.6069 Å2 / Biso min: 15.88 Å2
Baniso -1Baniso -2Baniso -3
1-4.1648 Å2-0 Å2-0 Å2
2--4.1648 Å2-0 Å2
3----8.3295 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1332 0 10 133 1475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061399
X-RAY DIFFRACTIONf_angle_d0.9871910
X-RAY DIFFRACTIONf_chiral_restr0.062214
X-RAY DIFFRACTIONf_plane_restr0.006251
X-RAY DIFFRACTIONf_dihedral_angle_d14.328518
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.66410.27211270.233125332660100
1.6641-1.73980.30531420.223625422684100
1.7398-1.83160.26841370.20325772714100
1.8316-1.94630.241400.188725502690100
1.9463-2.09660.24091480.182425612709100
2.0966-2.30750.20191360.17525832719100
2.3075-2.64130.25791480.196125842732100
2.6413-3.32740.22091410.188426442785100
3.3274-35.57770.19441330.1742705283897
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)
14.674-0.35860.42853.91860.74623.20140.0073-0.01710.13570.0423-0.17320.2896-0.0207-0.25410.13260.3047-0.045-0.04190.0943-0.01230.2263-5.049835.160117.7235
26.87125.1763-5.36527.658-6.98969.16540.05390.13950.1756-0.12750.18610.2746-0.0178-0.5158-0.22410.3304-0.0183-0.03760.1215-0.02090.17061.657840.841919.0107
30.6930.13291.03021.7951-0.24525.0104-0.0680.13780.0316-0.12870.12720.0128-0.32120.2576-0.05470.2958-0.01740.0540.19790.01590.22417.486248.8054.1436
41.3831-0.30561.69482.195-2.49356.68990.02860.3592-0.19160.0260.1966-0.51550.59621.59640.1030.21980.0871-0.0580.0898-0.05110.270810.986335.964414.2763
51.41770.30780.84630.17180.58362.95930.20210.09-0.2290.18-0.0023-0.13460.2260.146-0.1690.29580.0166-0.05010.1226-0.03230.22832.172631.254111.8748
68.80550.3665-1.91842.19853.51997.3613-0.2353-0.50671.0353-0.12730.03010.499-1.0153-0.96760.22420.35160.1469-0.05750.3711-0.00660.3766-14.26944.69571.9428
74.97911.77492.7062.32411.41325.0578-0.1723-0.15440.1167-0.0491-0.03940.5174-0.09510.00270.17530.2887-0.0340.05870.23320.02130.243-4.140846.62532.2046
82.3949-1.2202-0.28552.17120.01872.24120.09130.2172-0.15070.2791-0.0383-0.11360.6642-0.31450.04070.3365-0.0494-0.09620.1543-0.09050.2863-7.175828.59487.1154
95.9645-0.80625.07994.7661-0.4834.5810.1998-1.6888-0.67071.3674-0.10510.28510.7325-1.8345-0.0960.5902-0.3010.02340.39840.07180.2604-10.376428.925223.0173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:30)A5 - 30
2X-RAY DIFFRACTION2chain 'A' and (resseq 31:40)A31 - 40
3X-RAY DIFFRACTION3chain 'A' and (resseq 41:56)A41 - 56
4X-RAY DIFFRACTION4chain 'A' and (resseq 57:77)A57 - 77
5X-RAY DIFFRACTION5chain 'A' and (resseq 78:111)A78 - 111
6X-RAY DIFFRACTION6chain 'A' and (resseq 112:121)A112 - 121
7X-RAY DIFFRACTION7chain 'A' and (resseq 122:138)A122 - 138
8X-RAY DIFFRACTION8chain 'A' and (resseq 139:156)A139 - 156
9X-RAY DIFFRACTION9chain 'A' and (resseq 157:177)A157 - 177

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