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- PDB-3te9: 1.8 Angstrom Resolution Crystal Structure of K135M Mutant of Tran... -

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Basic information

Entry
Database: PDB / ID: 3te9
Title1.8 Angstrom Resolution Crystal Structure of K135M Mutant of Transaldolase B (TalA) from Francisella tularensis in Complex with Fructose 6-phosphate
ComponentsTransaldolase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Alpha-Beta Barrel/TIM Barrel / sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glyceronetransferase activity
Function / homology
Function and homology information


transaldolase / transaldolase activity / pentose-phosphate shunt, non-oxidative branch / carbohydrate metabolic process / cytosol
Similarity search - Function
Transaldolase type 1 / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FRUCTOSE -6-PHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Transaldolase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMinasov, G. / Light, S.H. / Halavaty, A. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Adherence to Burgi-Dunitz stereochemical principles requires significant structural rearrangements in Schiff-base formation: insights from transaldolase complexes.
Authors: Light, S.H. / Minasov, G. / Duban, M.E. / Anderson, W.F.
History
DepositionAug 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transaldolase
B: Transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,42512
Polymers76,9562
Non-polymers1,46810
Water10,989610
1
A: Transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9954
Polymers38,4781
Non-polymers5163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4308
Polymers38,4781
Non-polymers9527
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint6 kcal/mol
Surface area26640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.844, 86.730, 140.493
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transaldolase /


Mass: 38478.090 Da / Num. of mol.: 2 / Mutation: K135M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: FTT_1093c, talA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q5NFX0, transaldolase

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Non-polymers , 5 types, 620 molecules

#2: Chemical ChemComp-F6R / FRUCTOSE -6-PHOSPHATE / Fructose 6-phosphate


Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 610 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 9.4mG/mL, 0.5M Sodium chloride, 0.1M TRIS-HCl, 0.02M Fructose 6-phosphate; Screen: PEG's (H1), 0.2M Potassium/Sodium tartrate, 20% (w/v) PEG3350., pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 28, 2011 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 63010 / Num. obs: 63010 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 24.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3096 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IGX

3igx


Resolution: 1.8→29.58 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.729 / SU ML: 0.068
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19238 3187 5.1 %RANDOM
Rwork0.15836 ---
all0.16006 59591 --
obs0.16006 59591 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.432 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å2-0 Å2-0 Å2
2---0.1 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4867 0 95 610 5572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225245
X-RAY DIFFRACTIONr_bond_other_d0.0010.023548
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9827091
X-RAY DIFFRACTIONr_angle_other_deg0.86538791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4585667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03226.047215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.06315988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2181518
X-RAY DIFFRACTIONr_chiral_restr0.0870.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025740
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02936
X-RAY DIFFRACTIONr_mcbond_it1.0111.53255
X-RAY DIFFRACTIONr_mcbond_other0.3091.51307
X-RAY DIFFRACTIONr_mcangle_it1.79225305
X-RAY DIFFRACTIONr_scbond_it2.84531990
X-RAY DIFFRACTIONr_scangle_it4.6884.51785
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 234 -
Rwork0.187 4219 -
obs-4219 98.58 %
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)
11.5179-0.1851-0.14420.22060.40310.8199-0.0455-0.1237-0.06050.0912-0.00470.0310.14970.0140.05030.0472-0.01720.01430.05530.01260.01263.520722.374529.374
21.2604-0.6376-0.25940.9460.51320.3290.0098-0.22610.0162-0.00080.0548-0.08760.0477-0.001-0.06460.0559-0.0095-0.01190.06270.01260.018129.630121.334225.731
30.2939-0.0591-0.11930.1878-0.16580.4387-0.016-0.0297-0.0272-0.0406-0.0002-0.01760.0328-0.00490.01620.0196-0.00490.00880.0291-0.00080.030116.278920.346512.24
40.08750.0439-0.11140.2145-0.15660.28570.0250.00340.0090.039-0.01680.023-0.0492-0.0578-0.00810.02320.00480.00840.0469-0.01050.02041.797735.325817.6443
50.07680.0145-0.06610.1949-0.02650.24610.0004-0.0150.0396-0.01360.0118-0.0221-0.0361-0.0185-0.01220.0117-0.0046-0.0030.0336-0.00910.027713.63933.579514.3011
60.56030.31810.4640.54280.2810.3976-0.05690.05010.0442-0.03970.01150.0005-0.06960.03310.04540.05190.0009-0.01310.02010.00960.033827.104765.7483-14.5993
70.81590.4188-0.64612.86861.09261.40710.00720.24350.0479-0.0844-0.01090.0347-0.0782-0.38740.00370.00920.0321-0.00730.1896-0.01630.01115.323955.2238-23.7749
80.10480.1563-0.08050.2924-0.12530.5171-0.02220.0093-0.0059-0.0268-0.0088-0.02620.0317-0.00370.03110.028-0.0025-0.00020.0131-0.00020.02823.131747.5905-14.9344
90.15450.25770.07190.5092-0.01710.27420.0301-0.0106-0.00990.0939-0.0513-0.0303-0.07190.05250.02110.0416-0.0164-0.01550.0216-0.00380.02931.327559.4011-0.9883
100.0708-0.0328-0.08150.2407-0.25950.4919-0.02230.0131-0.02960.0611-0.0020.0121-0.0358-0.02840.02430.0312-0.0056-0.00990.0176-0.00140.037721.264349.7372-3.5271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 35
2X-RAY DIFFRACTION2A36 - 77
3X-RAY DIFFRACTION3A78 - 181
4X-RAY DIFFRACTION4A182 - 256
5X-RAY DIFFRACTION5A257 - 321
6X-RAY DIFFRACTION5A322
7X-RAY DIFFRACTION6B1 - 41
8X-RAY DIFFRACTION7B42 - 75
9X-RAY DIFFRACTION8B76 - 190
10X-RAY DIFFRACTION9B191 - 258
11X-RAY DIFFRACTION10B259 - 321

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