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- PDB-3ih0: Crystal structure of an uncharacterized sugar kinase PH1459 from ... -

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Basic information

Entry
Database: PDB / ID: 3ih0
TitleCrystal structure of an uncharacterized sugar kinase PH1459 from Pyrococcus horikoshii in complex with AMP-PNP
ComponentsUncharacterized sugar kinase PH1459
KeywordsTRANSFERASE / CARBOHYDRATE KINASE / PFKB FAMILY / PSI-II / 11207G / NYSGXRC / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / KINASE
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Putative sugar kinase PH1459
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKumar, G. / Eswaramoorthy, S. / 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 AMP-PNP
Authors: Kumar, G. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionJul 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Feb 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 1.4Sep 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 1.5Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3095
Polymers69,6182
Non-polymers6903
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-18 kcal/mol
Surface area24610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.170, 54.070, 77.720
Angle α, β, γ (deg.)90.00, 110.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21A-514-

HOH

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Components

#1: Protein Uncharacterized sugar kinase PH1459


Mass: 34809.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Top10 (Invitrogen) / Source: (gene. exp.) Pyrococcus horikoshii (archaea) / 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-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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 292 K / pH: 6.5
Details: 18% PEG 8000, 0.2M Magnesium ACETATE, 0.1M SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 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: 1.9→50 Å / Num. obs: 48828 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 15.6 Å2 / Rsym value: 0.075 / Net I/σ(I): 15
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 9.3 / Rsym value: 0.39 / % possible all: 97.5

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Processing

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

3ewm


Resolution: 1.9→29.64 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1884 -RANDOM
Rwork0.223 ---
obs0.223 47094 96.2 %-
all-47094 --
Displacement parametersBiso mean: 31.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.92 Å20 Å22.22 Å2
2--10.41 Å20 Å2
3----6.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4686 0 43 443 5172
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
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_it1.3661.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scbond_it2.2752
X-RAY DIFFRACTIONc_scangle_it3.4012.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.306 285 -
Rwork0.277 --
obs--88.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4amp-pnp.par
X-RAY DIFFRACTION5gol-param.txt

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