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Basic information

Entry
Database: PDB / ID: 4lca
TitleCrystal structure of probable sugar kinase protein from Rhizobium Etli CFN 42 complexed with thymidine
ComponentsProbable sugar kinase protein
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / sugar kinase / 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 / : / THYMIDINE / Probable sugar kinase protein
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 thymidine
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
DepositionJun 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 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 / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

Downloads & links

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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)79,35213
Polymers77,7002
Non-polymers1,65211
Water13,187732
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint10 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.525, 80.777, 82.663
Angle α, β, γ (deg.)90.000, 98.090, 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 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

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Non-polymers , 5 types, 743 molecules

#2: Chemical ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE / Thymidine


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N2O5
#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.: 732 / 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: 43.88 %
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 26, 2013
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 104115 / % possible obs: 94.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.082 / Χ2: 0.957 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.49-1.522.30.74441710.757175.9
1.52-1.542.70.748490.8188.2
1.54-1.572.90.61150090.81191.8
1.57-1.613.10.54751300.813193.3
1.61-1.643.20.49851700.819194.6
1.64-1.683.40.41852320.861195.4
1.68-1.723.40.36952980.879196
1.72-1.773.40.31952350.923195.8
1.77-1.823.40.26652560.976196
1.82-1.883.40.22452960.994196.2
1.88-1.943.40.17352691.02196.5
1.94-2.023.40.14753461.047196.5
2.02-2.113.40.12153081.067196.9
2.11-2.233.40.10653591.064197.4
2.23-2.373.50.09353911.004197.8
2.37-2.553.50.08353820.977197.9
2.55-2.83.40.07354180.974198
2.8-3.213.40.06154281.067197.8
3.21-4.043.20.05452441.073194.8
4.04-503.20.0553240.961194.3

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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: 1.5→40.18 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.259 / WRfactor Rwork: 0.2088 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8238 / SU B: 2.831 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0243 / SU Rfree: 0.0202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 5084 5 %RANDOM
Rwork0.1995 ---
obs0.2019 101974 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.65 Å2 / Biso mean: 24.4188 Å2 / Biso min: 10.36 Å2
Baniso -1Baniso -2Baniso -3
1-17.66 Å20 Å2-23.16 Å2
2---32.65 Å2-0 Å2
3---15 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5008 0 107 732 5847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195329
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.9947241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4955700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55123.684247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56715820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4481548
X-RAY DIFFRACTIONr_chiral_restr0.0850.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214086
X-RAY DIFFRACTIONr_mcbond_it1.9192.9862686
X-RAY DIFFRACTIONr_mcangle_it2.39840.5933367
X-RAY DIFFRACTIONr_scbond_it2.6073.5772643
X-RAY DIFFRACTIONr_rigid_bond_restr3.06135329
X-RAY DIFFRACTIONr_sphericity_free44.5895220
X-RAY DIFFRACTIONr_sphericity_bonded17.03455744
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 299 -
Rwork0.355 6442 -
all-6741 -
obs--86.26 %
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)
10.03690.00520.00820.0791-0.02610.1218-0.0007-0.00560.00240.01210.00090.0006-0.0073-0.0067-0.00020.00710.00210.00580.0263-0.00030.006867.083614.861338.2835
20.066-0.02210.02420.0801-0.01860.0277-0.00380.0005-0.00280.00460.00290.0039-0.0011-0.00290.00090.0048-0.00050.00660.02850.00020.009251.140627.71674.9578
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 328
2X-RAY DIFFRACTION2B-1 - 328

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