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- PDB-3lki: Crystal Structure of Fructokinase with bound ATP from Xylella fas... -

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Basic information

Entry
Database: PDB / ID: 3lki
TitleCrystal Structure of Fructokinase with bound ATP from Xylella fastidiosa
ComponentsFructokinase
KeywordsTRANSFERASE / Kinase / Fructokinase / ATP / Potassium ion / 11206h / 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
ADENOSINE-5'-TRIPHOSPHATE / : / PHOSPHATE ION / Fructokinase
Similarity search - Component
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLREP / Resolution: 2.04 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 with bound ATP from Xylella fastidiosa
Authors: Satyanarayana, L. / Burley, S.K. / Swaminathan, S.
History
DepositionJan 27, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 22, 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

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Assembly

Deposited unit
A: Fructokinase
B: Fructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2855
Polymers73,6442
Non-polymers6413
Water5,242291
1
B: Fructokinase
hetero molecules

A: Fructokinase


Theoretical massNumber of molelcules
Total (without water)74,2855
Polymers73,6442
Non-polymers6413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area3250 Å2
ΔGint-30 kcal/mol
Surface area26470 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-23 kcal/mol
Surface area26300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.221, 92.651, 179.765
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fructokinase /


Mass: 36821.961 Da / Num. of mol.: 2 / Fragment: sequence database residues 12-338
Source method: isolated from a genetically manipulated source
Details: Top10(Invitrogen) / Source: (gene. exp.) Xylella fastidiosa (bacteria) / Strain: Temecula1 / ATCC 700964 / Gene: 1143885, PD_1163 / Plasmid: pSGX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon + RIL / References: UniProt: Q87CC0, fructokinase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 3.97 Å3/Da / Density % sol: 69.02 %
Crystal growTemperature: 292 K / pH: 7
Details: 50mM Potassium Phosphate dihydrogen, 10% 1,4 Butanediol, 15% PEG 8000, 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
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: 2.04→50 Å / Num. obs: 75052 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 16.5 Å2 / Rsym value: 0.154 / Net I/σ(I): 5.8
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.78 / % possible all: 92.6

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLREP
Starting model: PDB ENTRY 3LJS
Resolution: 2.04→40.9 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2882 -RANDOM
Rwork0.213 ---
obs0.213 70744 93.7 %-
all-70744 --
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1-2.576 Å20 Å20 Å2
2---9.512 Å20 Å2
3---6.935 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.04→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4779 0 37 291 5107
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4871.5
X-RAY DIFFRACTIONc_mcangle_it2.4352
X-RAY DIFFRACTIONc_scbond_it2.4962
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shellResolution: 2.04→2.17 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.296 400 -
Rwork0.282 --
obs--81.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4ATP.pam.txt

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