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- PDB-3c8u: Crystal structure of putative fructose transport system kinase (Y... -

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Basic information

Entry
Database: PDB / ID: 3c8u
TitleCrystal structure of putative fructose transport system kinase (YP_612366.1) from Silicibacter sp. TM1040 at 1.95 A resolution
ComponentsFructokinase
KeywordsTRANSFERASE / YP_612366.1 / putative fructose transport system kinase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyfructokinase / fructokinase activity / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta / Fructokinase
Function and homology information
Biological speciesSilicibacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative fructose transport system kinase (YP_612366.1) from Silicibacter sp. TM1040 at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: 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 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructokinase


Theoretical massNumber of molelcules
Total (without water)22,7281
Polymers22,7281
Non-polymers00
Water5,188288
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.280, 102.280, 116.630
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

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Components

#1: Protein Fructokinase


Mass: 22728.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter sp. (bacteria) / Strain: TM1040 / Gene: YP_612366.1, TM1040_0371 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1GJR2, fructokinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: NANODROP, 23.1% PEG 3350, 0.214M Sodium fluoride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97978, 0.91837, 0.97964
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 13, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979781
20.918371
30.979641
ReflectionResolution: 1.95→35.267 Å / Num. obs: 15859 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.87 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 19.95
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.95-2.020.2637.2109581715199.9
2.02-2.10.18410.31120116821100
2.1-2.20.13912.5115101774199.4
2.2-2.310.116111258332120.5
2.31-2.460.08917.81212317821100
2.46-2.650.07220.31172917161100
2.65-2.910.06123.91148716871100
2.91-3.330.0527.91175017321100
3.33-4.190.04529.7105011618192.2
4.19-35.2670.03831.6117071822199.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→35.267 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.184 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.159
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. THE REFLECTIONS WITHIN RESOLUTION RANGES 3.70-3.64 AND 2.3-2.2 ANGSTROM WERE EXCLUDED DURING INTEGRATION AND SUBSEQUENT STEPS DUE TO THE PRESENCE OF ICE RINGS.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 792 5 %RANDOM
Rwork0.165 ---
obs0.167 15859 91.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.647 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.07 Å20 Å2
2---0.15 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.95→35.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1571 0 0 288 1859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221676
X-RAY DIFFRACTIONr_bond_other_d0.0010.021163
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9782297
X-RAY DIFFRACTIONr_angle_other_deg1.58232827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3985225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37423.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36115272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4961519
X-RAY DIFFRACTIONr_chiral_restr0.0850.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211923
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02344
X-RAY DIFFRACTIONr_mcbond_it1.80831058
X-RAY DIFFRACTIONr_mcbond_other0.5023424
X-RAY DIFFRACTIONr_mcangle_it2.97951696
X-RAY DIFFRACTIONr_scbond_it4.6168618
X-RAY DIFFRACTIONr_scangle_it6.911591
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 68 -
Rwork0.187 1182 -
all-1250 -
obs--99.76 %
Refinement TLS params.Method: refined / Origin x: 22.5935 Å / Origin y: 12.4151 Å / Origin z: 38.2847 Å
111213212223313233
T-0.0172 Å20.0401 Å20.0308 Å2--0.0276 Å20.0171 Å2---0.0186 Å2
L0.3968 °20.1923 °20.0372 °2-0.3713 °2-0.139 °2--0.3999 °2
S-0.0073 Å °0.0128 Å °0.0895 Å °-0.0321 Å °0.0305 Å °0.0572 Å °-0.0202 Å °-0.0292 Å °-0.0232 Å °

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