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- PDB-4jks: Crystal structure of probable sugar kinase protein from Rhizobium... -

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Basic information

Entry
Database: PDB / ID: 4jks
TitleCrystal structure of probable sugar kinase protein from Rhizobium etli CFN 42 complexed with DMSO, NYSGRC Target 14306
ComponentsProbable sugar kinase protein
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


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
ADENOSINE / Probable sugar kinase protein
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of probable sugar kinase protein from Rhizobium etli CFN 42 complexed with DMSO, NYSGRC Target 14306
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. ...Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C.
History
DepositionMar 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable sugar kinase protein
B: Probable sugar kinase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5478
Polymers77,7002
Non-polymers8476
Water11,097616
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint9 kcal/mol
Surface area24820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.830, 91.165, 92.429
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 Probable sugar kinase protein


Mass: 38849.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (bacteria) / Strain: CFN 42 / Gene: RHE_CH00135 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q2KDX6
#2: Chemical ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M AMMONIUM ACETATE, 0.1M BIS:TRIS:HCL, PH 6.5,25% PEG3350, soaked in 13% DMSO, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. obs: 107497 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.057 / Χ2: 0.981 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.51-1.547.253310.6341100
1.54-1.567.353050.65311000.797
1.56-1.597.353190.67111000.688
1.59-1.637.353360.68311000.591
1.63-1.667.353130.68711000.481
1.66-1.77.353160.70211000.41
1.7-1.747.353410.73811000.343
1.74-1.797.353310.76411000.271
1.79-1.847.353370.78611000.226
1.84-1.97.353380.83411000.175
1.9-1.977.353680.92211000.135
1.97-2.057.453460.96811000.112
2.05-2.147.453541.0511000.087
2.14-2.267.453891.09611000.077
2.26-2.47.353781.19511000.068
2.4-2.587.353991.39211000.064
2.58-2.847.354171.62311000.059
2.84-3.257.254431.505199.80.046
3.25-4.1754531.385199.20.034
4.1-506.956831.308199.10.032

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E3A

4e3a


Resolution: 1.51→41.22 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.2072 / WRfactor Rwork: 0.1701 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8654 / SU B: 1.197 / SU ML: 0.022 / SU R Cruickshank DPI: 0.0186 / SU Rfree: 0.0157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.019 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2017 5359 5 %RANDOM
Rwork0.1663 ---
obs0.168 107348 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.12 Å2 / Biso mean: 23.6828 Å2 / Biso min: 11.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0 Å2-0 Å2
2---0.26 Å2-0 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.51→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5008 0 54 616 5678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195325
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9827242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2925714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11224.023256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74615831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6771546
X-RAY DIFFRACTIONr_chiral_restr0.0770.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214121
X-RAY DIFFRACTIONr_rigid_bond_restr2.59235325
X-RAY DIFFRACTIONr_sphericity_free22.2385195
X-RAY DIFFRACTIONr_sphericity_bonded11.74155642
LS refinement shellResolution: 1.51→1.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 381 -
Rwork0.157 7430 -
all-7811 -
obs--99.71 %
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)
10.17810.0177-0.03130.1872-0.03980.1280.0057-0.0049-0.0070.00320.00160.00530.01290.0102-0.00730.0112-0.0025-0.00240.01560.00090.001213.7346-7.5369-20.4648
20.15640.04280.0540.28370.06750.15310.003-0.01990.00830.00630.00050.003-0.0133-0.0148-0.00350.0116-0.00140.00320.0166-0.00130.001326.720329.3683-20.3165
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 328
2X-RAY DIFFRACTION1A401 - 403
3X-RAY DIFFRACTION2B-1 - 328
4X-RAY DIFFRACTION2B401 - 403

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