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- PDB-3tbf: C-terminal domain of glucosamine-fructose-6-phosphate aminotransf... -

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Basic information

Entry
Database: PDB / ID: 3tbf
TitleC-terminal domain of glucosamine-fructose-6-phosphate aminotransferase from Francisella tularensis.
ComponentsGlucosamine--fructose-6-phosphate aminotransferase [isomerizing]
KeywordsTRANSFERASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / carbohydrate derivative binding / protein N-linked glycosylation / fructose 6-phosphate metabolic process / carbohydrate metabolic process / cytosol
Similarity search - Function
Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/AgaS, SIS domain 1 / GlmS/FrlB, SIS domain 2 / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain / SIS domain profile. ...Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/AgaS, SIS domain 1 / GlmS/FrlB, SIS domain 2 / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Nucleophile aminohydrolases, N-terminal / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsOsipiuk, J. / Zhou, M. / Maltseva, N. / Kim, Y. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: C-terminal domain of glucosamine-fructose-6-phosphate aminotransferase from Francisella tularensis.
Authors: Osipiuk, J. / Zhou, M. / Maltseva, N. / Kim, Y. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]
B: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]
C: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]
D: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]
E: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]
F: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]
G: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]
H: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]


Theoretical massNumber of molelcules
Total (without water)330,3948
Polymers330,3948
Non-polymers00
Water11,061614
1
A: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]
B: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]


Theoretical massNumber of molelcules
Total (without water)82,5992
Polymers82,5992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-16 kcal/mol
Surface area25610 Å2
MethodPISA
2
C: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]
D: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]


Theoretical massNumber of molelcules
Total (without water)82,5992
Polymers82,5992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-15 kcal/mol
Surface area25800 Å2
MethodPISA
3
E: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]
F: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]


Theoretical massNumber of molelcules
Total (without water)82,5992
Polymers82,5992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-14 kcal/mol
Surface area25770 Å2
MethodPISA
4
G: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]
H: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]


Theoretical massNumber of molelcules
Total (without water)82,5992
Polymers82,5992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-18 kcal/mol
Surface area26200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.370, 262.911, 83.797
Angle α, β, γ (deg.)90.000, 91.320, 90.000
Int Tables number4
Space group name H-MP1211
Detailschains A and B (or C-D or E-F or G-H)

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Components

#1: Protein
Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] / D-fructose-6-phosphate amidotransferase / GFAT / Glucosamine-6-phosphate synthase / Hexosephosphate ...D-fructose-6-phosphate amidotransferase / GFAT / Glucosamine-6-phosphate synthase / Hexosephosphate aminotransferase / L-glutamine-D-fructose-6-phosphate amidotransferase


Mass: 41299.293 Da / Num. of mol.: 8 / Fragment: C-terminal domain residues 241-612
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: FTT_0388, glmS / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5NHQ9, glutamine-fructose-6-phosphate transaminase (isomerizing)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsThe entire protein was used for crystallization. Chymotrypsin was used in crystallization droplets ...The entire protein was used for crystallization. Chymotrypsin was used in crystallization droplets which led to partial cleavage of the protein and crystallization of C-terminal domain. The prediction of the crystallized domain range, 241-612 residues, is based on predicted chymotrypsin cleavage sites generated by PeptideCutter website.

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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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M trimethylamine N-oxide, 20% PEG MME 2000, 0.1 M Tris buffer, chymotrypsin, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.28→45.8 Å / Num. all: 125776 / Num. obs: 125776 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.061 / Χ2: 0.797 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.28-2.342.50.4292.1152700.89776.2
2.34-2.382.70.456430.88881.7
2.38-2.432.90.39859220.90886.1
2.43-2.483.30.40361620.89788.9
2.48-2.533.40.36262000.90690.2
2.53-2.593.40.32662610.90290.9
2.59-2.663.40.25762550.88390.4
2.66-2.733.40.21761840.89390.1
2.73-2.813.40.18962200.91590.4
2.81-2.93.40.15362100.86990.1
2.9-33.40.11462360.87190
3-3.123.40.08562270.82690
3.12-3.263.50.07762000.81290.2
3.26-3.443.50.06162250.77490.4
3.44-3.653.50.04563310.71191.4
3.65-3.933.40.03665930.65695.6
3.93-4.333.50.03568090.72298.6
4.33-4.953.60.03569430.77199.8
4.95-6.243.60.03169010.62599.9
6.24-503.60.02169840.46999.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.28→45.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 14.506 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.784 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 5212 5 %RANDOM
Rwork0.1719 ---
all0.1749 104045 --
obs0.1749 104045 74.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 82.19 Å2 / Biso mean: 31.4268 Å2 / Biso min: 5.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0.14 Å2
2--0.12 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.28→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22165 0 0 614 22779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.0180.02222695
X-RAY DIFFRACTIONf_bond_other_d0.0010.0215140
X-RAY DIFFRACTIONf_angle_refined_deg1.5661.97630756
X-RAY DIFFRACTIONf_angle_other_deg0.934337428
X-RAY DIFFRACTIONf_dihedral_angle_1_deg6.02152904
X-RAY DIFFRACTIONf_dihedral_angle_2_deg36.69125.382929
X-RAY DIFFRACTIONf_dihedral_angle_3_deg17.842154165
X-RAY DIFFRACTIONf_dihedral_angle_4_deg16.1561571
X-RAY DIFFRACTIONf_chiral_restr0.090.23630
X-RAY DIFFRACTIONf_gen_planes_refined0.0060.0224939
X-RAY DIFFRACTIONf_gen_planes_other0.0010.024192
X-RAY DIFFRACTIONf_mcbond_it0.8971.514292
X-RAY DIFFRACTIONf_mcbond_other0.1921.55798
X-RAY DIFFRACTIONf_mcangle_it1.773223151
X-RAY DIFFRACTIONf_scbond_it2.71838403
X-RAY DIFFRACTIONf_scangle_it4.4824.57576
LS refinement shellResolution: 2.28→2.342 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 140 -
Rwork0.215 2638 -
all-2778 -
obs-2778 27.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1158-0.02340.03890.9552-0.12380.2478-0.00120.01140.01780.0459-0.00430.1634-0.02010.0070.00550.024-0.00950.02940.00920.00760.130772.652162.688928.2649
20.23680.0942-0.07451.61120.06230.3119-0.01-0.00070.02270.06960.02820.16420.0883-0.0415-0.01820.0577-0.00520.02240.01010.02320.130168.0917133.889830.3279
30.59320.0028-0.07570.71080.09190.02310.0191-0.0233-0.02460.0967-0.0094-0.01310.0110.0023-0.00970.1234-0.00280.03120.00880.00790.101657.207668.649747.0851
40.22350.36980.10191.05080.06090.21630.01510.03210.1140.0365-0.02410.1351-0.05580.00370.0090.1166-0.00510.02490.02910.02780.165257.593797.471842.2767
50.0557-0.03790.12690.2633-0.25260.43540.0006-0.0198-0.0175-0.1104-0.0338-0.08170.1139-0.04020.03320.0718-0.0050.04650.0350.01970.180935.7094159.852471.4536
60.0288-0.0170.02590.5994-0.12090.4024-0.032-0.01290.0345-0.0161-0.0341-0.1027-0.09910.03230.06610.0782-0.00240.01290.0233-0.00010.200541.0891188.607771.7693
70.0146-0.12760.04221.8967-0.37020.14720.0121-0.0024-0.0216-0.10920.0107-0.0530.06420.0034-0.02280.1312-0.0061-0.02160.02450.02040.202619.689994.644983.9053
80.39990.18340.00521.5182-0.06390.24930.0155-0.00510.0253-0.0332-0.0131-0.24570.02690.0145-0.00240.1259-0.0305-0.02430.01890.01720.15321.9904123.449779.4259
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A246 - 602
2X-RAY DIFFRACTION2B245 - 602
3X-RAY DIFFRACTION3C245 - 602
4X-RAY DIFFRACTION4D245 - 601
5X-RAY DIFFRACTION5E245 - 602
6X-RAY DIFFRACTION6F245 - 602
7X-RAY DIFFRACTION7G246 - 602
8X-RAY DIFFRACTION8H244 - 602

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