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- PDB-4k8c: Crystal structure of probable sugar kinase protein from Rhizobium... -

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Basic information

Entry
Database: PDB / ID: 4k8c
TitleCrystal structure of probable sugar kinase protein from Rhizobium etli CFN 42 complexed with ADP
Componentssugar kinase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCHCONSORTIUM / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


phosphotransferase activity, alcohol group as acceptor / 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 / ADENOSINE-5'-DIPHOSPHATE / : / 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 ADP
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
DepositionApr 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,48012
Polymers77,7002
Non-polymers1,78010
Water12,899716
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-5 kcal/mol
Surface area24400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.399, 80.847, 83.499
Angle α, β, γ (deg.)90.000, 98.480, 90.000
Int Tables number4
Space group name H-MP1211
Detailsdimeric

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein sugar kinase


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

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Non-polymers , 5 types, 726 molecules

#2: Chemical ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: 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
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 44.3 %
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, 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: Apr 12, 2013
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. obs: 100789 / % possible obs: 95.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.068 / Χ2: 0.959 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.51-1.543.50.32852500.859199.8
1.54-1.563.60.28152470.922199.9
1.56-1.593.70.2553120.961100
1.59-1.633.70.2252510.9361100
1.63-1.663.70.19952961.0031100
1.66-1.73.70.1852610.9851100
1.7-1.743.70.15952950.9731100
1.74-1.793.70.1452740.9731100
1.79-1.843.70.12553130.9721100
1.84-1.93.60.11650640.975196.1
1.9-1.973.10.10642141.119179.6
1.97-2.053.70.08952650.92199.9
2.05-2.143.70.07853170.9411100
2.14-2.263.60.07640340.961176.4
2.26-2.43.60.06846430.968187.7
2.4-2.583.70.06452980.943199.7
2.58-2.843.70.0652780.916199.4
2.84-3.253.50.05551661.01197.2
3.25-4.13.20.05139890.962174.8
4.1-503.30.05250220.943192.3

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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-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E3A

4e3a


Resolution: 1.51→36.77 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2698 / WRfactor Rwork: 0.2198 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8392 / SU B: 2.491 / SU ML: 0.046 / SU R Cruickshank DPI: 0.026 / SU Rfree: 0.0206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE RESIDUAL FLAT DENSITY BETWEEN ILE-307 AND SER-245 IS DUE TO THE TRACE AMOUNTS OF EXOGENOUS ADP OR ITS ANALOGS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 5011 5 %RANDOM
Rwork0.2085 ---
obs0.2106 100681 94.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.33 Å2 / Biso mean: 18.1073 Å2 / Biso min: 6.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å2-3.58 Å2
2---0.13 Å2-0 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.51→36.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5008 0 110 716 5834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195353
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9957285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6765706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53123.655249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59315825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4931549
X-RAY DIFFRACTIONr_chiral_restr0.0860.2819
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214099
X-RAY DIFFRACTIONr_rigid_bond_restr2.44835353
X-RAY DIFFRACTIONr_sphericity_free29.0215220
X-RAY DIFFRACTIONr_sphericity_bonded11.27255750
LS refinement shellResolution: 1.509→1.548 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 387 -
Rwork0.186 7275 -
all-7662 -
obs--98.48 %
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)
10.2440.06550.05220.3312-0.08090.42980.0037-0.0160.0090.02950.00640.0186-0.0096-0.0227-0.01010.00950.00230.01050.00310.00210.012766.533114.87138.5307
20.2237-0.0850.1150.2572-0.05180.2506-0.0120.0148-0.01450.00780.00960.0195-0.0053-0.01050.00240.0096-0.00140.01660.02410.00190.030550.794327.73745.128
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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