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- PDB-1xc3: Structure of a Putative Fructokinase from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1xc3
TitleStructure of a Putative Fructokinase from Bacillus subtilis
ComponentsPutative fructokinase
KeywordsTRANSFERASE / reductively methylated / fructokinase / Zn-coordiation / structural genomics / protein structure initiative / MCSG / PSI / Midwest Center for Structural Genomics
Function / homology
Function and homology information


fructokinase / fructokinase activity / polysaccharide catabolic process / ATP binding / metal ion binding
Similarity search - Function
: / : / ROK family signature. / ROK family / ROK family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Putative fructokinase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsCuff, M.E. / Quartey, P. / Lezondra, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural studies of ROK fructokinase YdhR from Bacillus subtilis: insights into substrate binding and fructose specificity.
Authors: Nocek, B. / Stein, A.J. / Jedrzejczak, R. / Cuff, M.E. / Li, H. / Volkart, L. / Joachimiak, A.
History
DepositionAug 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 10, 2012Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT FOR THE PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative fructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3826
Polymers32,7421
Non-polymers6405
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative fructokinase
hetero molecules

A: Putative fructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,76412
Polymers65,4842
Non-polymers1,28010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5780 Å2
ΔGint-96 kcal/mol
Surface area23620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)112.660, 112.660, 75.087
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-499-

HOH

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Components

#1: Protein Putative fructokinase


Mass: 32742.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ydhR / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: O05510, fructokinase
#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Ammonium sulfate, Tris, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 23, 2004 / Details: SBC2
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→95.35 Å / Num. all: 30770 / Num. obs: 29850 / % possible obs: 97.01 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.155 Å / % possible all: 98.32

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
PHENIXphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→95.35 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.16 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.127
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20283 1603 5.1 %RANDOM
Rwork0.18029 ---
all0.18145 30770 --
obs0.18145 29850 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.664 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.06 Å20 Å2
2---0.11 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.1→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 15 221 2490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222350
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.9633186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8515300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0224.5100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82415382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.346159
X-RAY DIFFRACTIONr_chiral_restr0.0820.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021793
X-RAY DIFFRACTIONr_nbd_refined0.1950.21128
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21630
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2210
X-RAY DIFFRACTIONr_metal_ion_refined0.0310.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.226
X-RAY DIFFRACTIONr_mcbond_it0.7381.51515
X-RAY DIFFRACTIONr_mcangle_it1.27922360
X-RAY DIFFRACTIONr_scbond_it1.7643959
X-RAY DIFFRACTIONr_scangle_it2.8844.5826
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 103 -
Rwork0.226 2236 -
obs--98.32 %

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