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- PDB-3tkf: 1.5 Angstrom Resolution Crystal Structure of K135M Mutant of Tran... -

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Basic information

Entry
Database: PDB / ID: 3tkf
Title1.5 Angstrom Resolution Crystal Structure of K135M Mutant of Transaldolase B (TalA) from Francisella tularensis in Complex with Sedoheptulose 7-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 / cytoplasm
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
D-ALTRO-HEPT-2-ULOSE 7-PHOSPHATE / DI(HYDROXYETHYL)ETHER / Transaldolase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)79,32516
Polymers76,9562
Non-polymers2,36814
Water13,799766
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint15 kcal/mol
Surface area27510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.827, 87.194, 141.136
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, 780 molecules

#2: Chemical ChemComp-I22 / D-ALTRO-HEPT-2-ULOSE 7-PHOSPHATE / 7-O-PHOSPHONO-D-ALTRO-HEPT-2-ULOSE / SEDOHEPTULOSE 7-PHOSPHATE


Mass: 290.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15O10P
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / 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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein:9.4mG/mL, 0.5M Sodium chloride, 0.1M TRIS-HCl (pH 8.3), 0.015M Sedoheptulose 7-phosphate; Screen: PEG's (B6), 0.1M HEPES, 25% (w/v) PEG2000 MME., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2011 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 109948 / Num. obs: 109948 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 23.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 3.7 / Num. unique all: 5431 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TE9

3te9


Resolution: 1.5→29.67 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.908 / SU ML: 0.033
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15866 5459 5 %RANDOM
Rwork0.14384 ---
all0.14459 103476 --
obs0.14459 103476 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.896 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å2-0 Å2-0 Å2
2--0.17 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4867 0 151 766 5784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225414
X-RAY DIFFRACTIONr_bond_other_d0.0010.023664
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9967350
X-RAY DIFFRACTIONr_angle_other_deg0.97439105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9775693
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70626.261222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.397151017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2981518
X-RAY DIFFRACTIONr_chiral_restr0.0940.2859
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025943
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02949
X-RAY DIFFRACTIONr_mcbond_it1.0941.53326
X-RAY DIFFRACTIONr_mcbond_other0.3441.51331
X-RAY DIFFRACTIONr_mcangle_it1.96325442
X-RAY DIFFRACTIONr_scbond_it3.08932088
X-RAY DIFFRACTIONr_scangle_it5.0824.51906
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 404 -
Rwork0.208 7578 -
obs-7578 99.97 %
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)
11.1544-0.15540.14320.0141-0.3030.8745-0.0533-0.11780.04380.03120.0174-0.0099-0.13480.00230.0360.0233-0.0062-0.01290.0472-0.01120.009924.008521.070529.4097
20.9536-0.37920.20260.5102-0.18030.339-0.0065-0.15410.0259-0.06220.03020.0587-0.0490.0019-0.02370.00210.015-0.0040.0601-0.00730.0227-2.359922.362125.74
30.2536-0.05660.06870.11460.10670.4481-0.0324-0.01860.0378-0.03830.01470.0169-0.03780.00790.01770.0189-0.0059-0.01420.02240.00080.031411.119723.210312.214
40.19030.04190.09980.06580.1090.3330.0178-0.0128-0.01280.0306-0.0113-0.03050.04060.0559-0.00640.02280.0039-0.00780.03580.01030.017925.47577.873717.8082
50.07210.06270.04310.14470.00380.2245-0.0159-0.0156-0.021-0.01850.01680.0240.03370.0147-0.00090.01010.00240.00330.03420.00250.017813.71979.767214.2785
60.59810.2309-0.1830.3191-0.02340.1061-0.03410.0374-0.0114-0.02220.00020.03060.0720.02680.03390.0505-0.00220.01120.0186-0.0060.0250.0588-22.6543-14.8927
70.18230.07030.78112.184-0.87661.6119-0.05280.1796-0.0828-0.08130.1491-0.22970.03640.4051-0.09630.00980.01490.04150.1328-0.03780.000922.2748-12.5112-23.6018
80.1220.20290.110.25230.13150.4076-0.03490.01280.0223-0.03230.00940.0487-0.02850.03360.02550.0288-0.0084-0.00670.01470.00180.02194.3949-4.3521-14.9957
90.16720.2514-0.1090.4149-0.03960.10390.0455-0.01650.0180.0415-0.05350.03640.06-0.03680.0080.0397-0.02010.01220.0146-0.00150.0305-3.8891-16.168-1.098
10-0.0647-0.03060.16610.26280.25490.3256-0.0156-0.00390.02340.053-0.00720.01320.00860.03640.02280.0202-0.00320.01320.0167-0.00130.02665.9793-6.5023-3.6036
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 DIFFRACTION6B1 - 41
7X-RAY DIFFRACTION7B42 - 75
8X-RAY DIFFRACTION8B76 - 190
9X-RAY DIFFRACTION9B191 - 258
10X-RAY DIFFRACTION10B259 - 321

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