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- PDB-3gbu: Crystal structure of an uncharacterized sugar kinase PH1459 from ... -

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Basic information

Entry
Database: PDB / ID: 3gbu
TitleCrystal structure of an uncharacterized sugar kinase PH1459 from Pyrococcus horikoshii in complex with ATP
ComponentsUncharacterized sugar kinase PH1459
KeywordsTRANSFERASE / CARBOHYDRATE KINASE / PFKB FAMILY / PSI-II / 11207g / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York Structural GenomiX Research Consortium / Kinase / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / fructokinase activity / fructose metabolic process / ATP binding
Similarity search - Function
Ribokinase/fructokinase / 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 / Putative sugar kinase PH1459
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEswaramoorthy, S. / Kumar, G. / Zhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of an uncharacterized sugar kinase PH1459 from Pyrococcus horikoshii in complex with ATP
Authors: Eswaramoorthy, S. / Kumar, G. / Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionFeb 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 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: Uncharacterized sugar kinase PH1459
B: Uncharacterized sugar kinase PH1459
C: Uncharacterized sugar kinase PH1459
D: Uncharacterized sugar kinase PH1459
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,2668
Polymers139,2374
Non-polymers2,0294
Water8,917495
1
A: Uncharacterized sugar kinase PH1459
D: Uncharacterized sugar kinase PH1459
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6334
Polymers69,6182
Non-polymers1,0142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-14.4 kcal/mol
Surface area25270 Å2
MethodPISA
2
B: Uncharacterized sugar kinase PH1459
C: Uncharacterized sugar kinase PH1459
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6334
Polymers69,6182
Non-polymers1,0142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-13.5 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.148, 119.422, 178.810
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
Uncharacterized sugar kinase PH1459


Mass: 34809.219 Da / Num. of mol.: 4 / Fragment: UNP residues 8-309 / Mutation: C225F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1459, PHCC008 / Plasmid: pSGX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL
References: UniProt: O59128, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsBOTH THE ELECTRON DENSITY AND MASS SPECTROSCOPY CONFIRM THAT THERE IS A MUTATION C225F.

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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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG 8000, 0.2M Calcium acetate, 0.1M Sodium cacodylate pH 6.5, ATP, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / 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: 2.2→50 Å / Num. all: 78203 / Num. obs: 78203 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 29.1 Å2 / Net I/σ(I): 3.2

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EWM

3ewm


Resolution: 2.2→49.66 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1369707.14 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3946 5.1 %RANDOM
Rwork0.216 ---
all0.216 78107 --
obs0.216 78107 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.9905 Å2 / ksol: 0.349262 e/Å3
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å20 Å2
2--3.67 Å20 Å2
3----5.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→49.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9344 0 124 495 9963
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 644 5 %
Rwork0.256 12184 -
obs-12184 100 %

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