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- PDB-3f7w: Crystal structure of putative fructosamine-3-kinase (YP_290396.1)... -

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Basic information

Entry
Database: PDB / ID: 3f7w
TitleCrystal structure of putative fructosamine-3-kinase (YP_290396.1) from THERMOBIFIDA FUSCA YX-ER1 at 1.85 A resolution
Componentsputative fructosamine-3-kinase
KeywordsTRANSFERASE / YP_290396.1 / putative fructosamine-3-kinase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Unknown function
Function / homology
Function and homology information


Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #240 / Fructosamine/Ketosamine-3-kinase / Fructosamine kinase / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase-like domain superfamily / Up-down Bundle ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #240 / Fructosamine/Ketosamine-3-kinase / Fructosamine kinase / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Unknown ligand / Fructosamine kinase
Similarity search - Component
Biological speciesThermobifida fusca YX (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative fructosamine-3-kinase (YP_290396.1) from THERMOBIFIDA FUSCA YX-ER1 at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 10, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionNov 25, 2008ID: 3D1U
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 27, 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

Downloads & links

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Assembly

Deposited unit
A: putative fructosamine-3-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,29210
Polymers31,8041
Non-polymers4879
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.178, 91.178, 82.049
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsAUTHORS STATE THAT ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY AND CRYSTAL PACKING ANALYSIS SUPPORT THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION

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Components

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Protein , 1 types, 1 molecules A

#1: Protein putative fructosamine-3-kinase


Mass: 31804.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca YX (bacteria)
Description: Genomic DNA from the protease deficient ER-1 strain derived form Thermobifida fusca YX was a gift from David Wilson.
Gene: Tfu_2340, YP_290396.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q47ME9

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Non-polymers , 5 types, 332 molecules

#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 1.0000M LiCl, 10.0000% PEG-6000, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.918381,0.979224,0.978618
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2008
Details: 1m long Rh coated bent cylindrical mirror forhorizontal and vertical focussing
RadiationMonochromator: Double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9183811
20.9792241
30.9786181
ReflectionResolution: 1.85→28.916 Å / Num. obs: 30125 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 28.539 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 7.325
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.97.20.6831.11574221990.683100
1.9-1.957.20.5371.41515421180.537100
1.95-2.017.20.4181.81490720780.418100
2.01-2.077.20.312.41449120190.31100
2.07-2.147.10.223.41393619550.22100
2.14-2.217.20.1664.61363119050.166100
2.21-2.297.10.1474.71300918330.147100
2.29-2.397.10.1186.31263117820.118100
2.39-2.497.10.1076.41208317050.107100
2.49-2.6270.0927.61144316290.092100
2.62-2.7670.088.51086315510.0899.9
2.76-2.936.90.0689.81025614790.068100
2.93-3.136.90.06210.4959913900.062100
3.13-3.386.80.05810.7882812980.05899.8
3.38-3.76.60.05111.2794712090.051100
3.7-4.146.20.04712.6686911010.04799.8
4.14-4.786.60.04314.163589630.04397.9
4.78-5.856.90.04114.758438430.041100
5.85-8.276.70.03716.745156740.037100
8.27-28.925.90.02920.723173940.02997

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→28.916 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.725 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.119
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. CL IONS AND PEG6000 FRAGMENT (PEG) FROM CRYSTALLIZATION AND ETHYLENE GLYCOL (EDO) FROM CRYO SOLUTION WERE MODELED. 5. THERE IS UNIDENTIFIED DENSITY FOUND NEAR ATP BINDING SITE. IT WAS MODELED AS AN UNKNOWN LIGAND (UNL).
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1522 5.1 %RANDOM
Rwork0.165 ---
obs0.167 30072 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.45 Å2 / Biso mean: 32.77 Å2 / Biso min: 17.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.85→28.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 35 323 2588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212485
X-RAY DIFFRACTIONr_bond_other_d0.0020.021699
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9543404
X-RAY DIFFRACTIONr_angle_other_deg0.95734077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.495318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.25422.258124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33715353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5291530
X-RAY DIFFRACTIONr_chiral_restr0.0810.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022908
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02553
X-RAY DIFFRACTIONr_nbd_refined0.2170.2507
X-RAY DIFFRACTIONr_nbd_other0.2020.21817
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21191
X-RAY DIFFRACTIONr_nbtor_other0.0850.21273
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2222
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.225
X-RAY DIFFRACTIONr_mcbond_it1.8331592
X-RAY DIFFRACTIONr_mcbond_other0.4473614
X-RAY DIFFRACTIONr_mcangle_it2.57252470
X-RAY DIFFRACTIONr_scbond_it4.24681038
X-RAY DIFFRACTIONr_scangle_it5.70611934
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 95 -
Rwork0.224 2102 -
all-2197 -
obs--99.95 %
Refinement TLS params.Method: refined / Origin x: 61.3176 Å / Origin y: 11.2604 Å / Origin z: 7.7484 Å
111213212223313233
T-0.1022 Å2-0.0007 Å2-0.0033 Å2--0.0427 Å20.0175 Å2---0.0664 Å2
L0.7345 °20.0587 °20.0177 °2-1.1581 °2-0.0911 °2--1.443 °2
S-0.0027 Å °0.1168 Å °0.015 Å °-0.0857 Å °0.0043 Å °0.0048 Å °0.0743 Å °0.059 Å °-0.0016 Å °

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