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- PDB-5htj: Putative sugar kinases from Synechococcus elongatus PCC7942-D8A -

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Basic information

Entry
Database: PDB / ID: 5htj
TitlePutative sugar kinases from Synechococcus elongatus PCC7942-D8A
ComponentsProbable sugar kinase
KeywordsTRANSFERASE / sugar kinases / Synechococcus elongatus PCC7942-D8A / mutation
Function / homology
Function and homology information


D-ribulokinase / D-ribulokinase activity / xylulose metabolic process / D-xylulokinase activity / ATP binding / cytosol
Similarity search - Function
Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsXie, Y. / Li, M. / Chang, W.
CitationJournal: Plos One / Year: 2016
Title: Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana
Authors: Xie, Y. / Li, M. / Chang, W.
History
DepositionJan 26, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Refinement description
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable sugar kinase


Theoretical massNumber of molelcules
Total (without water)47,2631
Polymers47,2631
Non-polymers00
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.942, 46.920, 88.644
Angle α, β, γ (deg.)90.00, 91.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Probable sugar kinase


Mass: 47263.227 Da / Num. of mol.: 1 / Mutation: D8A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / Gene: Synpcc7942_2462 / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q31KC7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BIS-TRIS pH 6.5, 20% w/v Polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 28525 / % possible obs: 99.76 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 23.947
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 4.629 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.001→33.834 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.34
RfactorNum. reflection% reflection
Rfree0.233 2008 7.04 %
Rwork0.2066 --
obs0.2085 28508 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.001→33.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3193 0 0 477 3670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083275
X-RAY DIFFRACTIONf_angle_d1.0444476
X-RAY DIFFRACTIONf_dihedral_angle_d13.091169
X-RAY DIFFRACTIONf_chiral_restr0.038499
X-RAY DIFFRACTIONf_plane_restr0.005588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.001-2.0510.29231390.25821862X-RAY DIFFRACTION99
2.051-2.10650.31471450.26551843X-RAY DIFFRACTION100
2.1065-2.16850.26351460.24871905X-RAY DIFFRACTION100
2.1685-2.23850.30821400.25261898X-RAY DIFFRACTION100
2.2385-2.31840.29281450.26751848X-RAY DIFFRACTION100
2.3184-2.41120.29041460.24771882X-RAY DIFFRACTION100
2.4112-2.52090.23761390.24811891X-RAY DIFFRACTION100
2.5209-2.65380.26191420.24241882X-RAY DIFFRACTION100
2.6538-2.820.27871490.22971894X-RAY DIFFRACTION100
2.82-3.03760.23061380.22311887X-RAY DIFFRACTION100
3.0376-3.3430.21841450.20491921X-RAY DIFFRACTION100
3.343-3.82620.19891390.17541885X-RAY DIFFRACTION100
3.8262-4.81840.18451420.15231929X-RAY DIFFRACTION100
4.8184-33.83920.19891530.17591973X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 28.6266 Å / Origin y: 4.6171 Å / Origin z: 20.8085 Å
111213212223313233
T0.1961 Å20.0112 Å2-0.022 Å2-0.1806 Å2-0.0426 Å2--0.2265 Å2
L0.6014 °2-0.0286 °2-0.4059 °2-0.4891 °2-0.1121 °2--1.6353 °2
S0.0193 Å °0.0874 Å °-0.0626 Å °-0.0482 Å °-0.0638 Å °0.0787 Å °-0.0754 Å °-0.1089 Å °0.0489 Å °
Refinement TLS groupSelection details: all

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