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- PDB-5htp: Putative sugar kinases from Synechococcus elongatus PCC7942 in co... -

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Basic information

Entry
Database: PDB / ID: 5htp
TitlePutative sugar kinases from Synechococcus elongatus PCC7942 in complex with AMPPNP
ComponentsProbable sugar kinase
KeywordsTRANSFERASE / putative sugar kinases / Synechococcus elongatus PCC7942 / AMPPNP / complex
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / D-ribulose kinase
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 27, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8132
Polymers47,3071
Non-polymers5061
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-1 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.515, 46.567, 87.991
Angle α, β, γ (deg.)90.00, 91.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Probable sugar kinase


Mass: 47307.238 Da / Num. of mol.: 1
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: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 46.58 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 18681 / % possible obs: 98.9 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.18
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 1.79 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24.707 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.27
RfactorNum. reflection% reflection
Rfree0.2327 1848 9.9 %
Rwork0.1935 --
obs0.1975 18666 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→24.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 31 146 3373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053311
X-RAY DIFFRACTIONf_angle_d0.8864532
X-RAY DIFFRACTIONf_dihedral_angle_d14.9491181
X-RAY DIFFRACTIONf_chiral_restr0.032505
X-RAY DIFFRACTIONf_plane_restr0.004590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3003-2.36250.31891430.27471283X-RAY DIFFRACTION97
2.3625-2.4320.28431410.25191266X-RAY DIFFRACTION100
2.432-2.51040.30611410.2511311X-RAY DIFFRACTION100
2.5104-2.60.37791410.2461305X-RAY DIFFRACTION100
2.6-2.7040.29441360.25061301X-RAY DIFFRACTION99
2.704-2.82690.23791450.23561278X-RAY DIFFRACTION100
2.8269-2.97570.29461480.23451291X-RAY DIFFRACTION99
2.9757-3.16180.24771410.21361291X-RAY DIFFRACTION99
3.1618-3.40530.26021400.18611294X-RAY DIFFRACTION100
3.4053-3.7470.20221410.17461297X-RAY DIFFRACTION98
3.747-4.28670.221450.16941290X-RAY DIFFRACTION98
4.2867-5.39150.18891420.15851296X-RAY DIFFRACTION98
5.3915-24.70820.17231440.16171315X-RAY DIFFRACTION95

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