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- PDB-3ljs: Crystal structure of Fructokinase from Xylella fastidiosa -

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Basic information

Entry
Database: PDB / ID: 3ljs
TitleCrystal structure of Fructokinase from Xylella fastidiosa
ComponentsFructokinase
KeywordsTRANSFERASE / Fructokianse / Kinase / PSI2 / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


kinase activity / phosphorylation / ATP binding
Similarity search - Function
pfkB family of carbohydrate kinases signature 1. / 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
PHOSPHATE ION / Fructokinase
Similarity search - Component
Biological speciesXylella fastidiosa Temecula1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsSatyanarayana, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of Fructokinase from Xylella fastidiosa
Authors: Satyanarayana, L. / Burley, S.K. / Swaminathan, S.
History
DepositionJan 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Fructokinase
B: Fructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7393
Polymers73,6442
Non-polymers951
Water5,567309
1
B: Fructokinase
hetero molecules

A: Fructokinase


Theoretical massNumber of molelcules
Total (without water)73,7393
Polymers73,6442
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area2170 Å2
ΔGint-24 kcal/mol
Surface area27020 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-17 kcal/mol
Surface area26980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.019, 93.625, 179.439
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDimer

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Components

#1: Protein Fructokinase /


Mass: 36821.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Top10 cells (Invitrogen)
Source: (gene. exp.) Xylella fastidiosa Temecula1 (bacteria)
Strain: Temecula1 / ATCC 700964 / Gene: 1143885, PD_1163 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CODON + RIL / References: UniProt: Q87CC0, fructokinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 3.99 Å3/Da / Density % sol: 69.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30mM Potassium Phosphate Dihydrogen 15% PEG 8K , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. all: 83152 / Num. obs: 83152 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 17.6 Å2 / Rsym value: 0.135 / Net I/σ(I): 7.1
Reflection shellResolution: 1.97→2.05 Å / Redundancy: 12 % / Mean I/σ(I) obs: 6.4 / Num. unique all: 7745 / Rsym value: 0.63 / % possible all: 49.1

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXCDphasing
SHARPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.97→40.46 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3173 -RANDOM
Rwork0.209 ---
all0.23 78870 --
obs0.209 78870 94.2 %-
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.71 Å20 Å20 Å2
2--11.69 Å20 Å2
3----6.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.97→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4793 0 5 309 5107
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_degree23.5
X-RAY DIFFRACTIONc_improper_angle_deg0.77
LS refinement shellResolution: 1.93→2.05 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.298 281 -
Rwork0.287 --
obs-6959 49.1 %

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