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- PDB-3upb: 1.5 Angstrom Resolution Crystal Structure of Transaldolase from F... -

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Basic information

Entry
Database: PDB / ID: 3upb
Title1.5 Angstrom Resolution Crystal Structure of Transaldolase from Francisella tularensis in Covalent Complex with Arabinose-5-Phosphate
ComponentsTransaldolase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Alpha-Beta Barrel/TIM Barrel
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
ARABINOSE-5-PHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Transaldolase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLight, S.H. / Minasov, G. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Struct.Funct.Genom. / Year: 2014
Title: Arabinose 5-phosphate covalently inhibits transaldolase.
Authors: Light, S.H. / Anderson, W.F.
History
DepositionNov 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 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_conn / 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_conn.pdbx_leaving_atom_flag / _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)78,2119
Polymers76,9522
Non-polymers1,2597
Water13,025723
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-10 kcal/mol
Surface area25580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.045, 86.197, 140.547
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: 38476.074 Da / Num. of mol.: 2
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, 730 molecules

#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-A5P / ARABINOSE-5-PHOSPHATE


Mass: 232.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13O8P
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 723 / 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: 43.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 11.2 mg/ml, 0.5 M sodium chloride, 0.01 M Tris-HCl, Screen: Pegs H1 (Qiagen), 0.2 M K/Na tartrate, 20% (w/v) PEG 3350 Crystals were soaked in a mother liquor containing 20 mM ...Details: Protein: 11.2 mg/ml, 0.5 M sodium chloride, 0.01 M Tris-HCl, Screen: Pegs H1 (Qiagen), 0.2 M K/Na tartrate, 20% (w/v) PEG 3350 Crystals were soaked in a mother liquor containing 20 mM arabinose-5-phosphate for 2 hours before being flash frozen for data collection, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2011 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 106919 / Num. obs: 106919 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 4 / Num. unique all: 5295 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3IGX

3igx


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.939 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17527 5316 5 %RANDOM
Rwork0.15056 ---
all0.15181 106919 --
obs0.15181 101536 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.775 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4847 0 79 723 5649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.025210
X-RAY DIFFRACTIONr_bond_other_d0.0010.023556
X-RAY DIFFRACTIONr_angle_refined_deg2.0571.9877073
X-RAY DIFFRACTIONr_angle_other_deg1.0438846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4075686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25926.182220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.269151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2721519
X-RAY DIFFRACTIONr_chiral_restr0.1260.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02921
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 345 -
Rwork0.202 6707 -
obs--94.73 %
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)
10.2079-0.01240.22680.1182-0.01050.3031-0.0830.0453-0.0152-0.00090.02290.0004-0.14540.02830.06010.156-0.0183-0.04220.1046-0.00490.125-1.037422.5427-14.5954
23.99070.1914-1.63737.35473.62882.63860.44650.92520.3657-0.4322-0.44350.2934-0.4445-0.8233-0.0030.1640.2087-0.03080.64320.05870.0821-22.737812.5689-24.9235
30.10130.0775-0.00170.2772-0.12840.6087-0.05060.0154-0.0196-0.03890.0066-0.02780.0336-0.01780.0440.1173-0.00930.00610.1008-0.00290.0998-5.50313.3552-17.6389
40.23250.22560.25580.37540.15620.34420.00380.00460.02070.0611-0.05010.0054-0.05250.05180.04620.1249-0.0317-0.00530.1049-0.00770.10932.902215.9749-1.2081
50.01370.051-0.07640.2348-0.34560.54930.0021-0.0168-0.01180.0505-0.0377-0.0072-0.03780.00650.03560.113-0.013-0.00660.1072-0.00130.1127-3.75894.0515-1.1491
613.6274-2.18566.08261.01421.719313.66730.50830.1828-0.442-0.1666-0.25050.0632-0.0972-0.7397-0.25780.04810.0805-0.05550.2691-0.06510.1249-27.63819.8101-17.6328
70.46150.0322-0.44120.0077-0.05130.8498-0.0185-0.1032-0.02170.0148-0.0137-0.00130.10820.04650.03220.1172-0.02710.00860.14060.0040.0872-19.8082-19.845128.4047
82.7922-0.996-1.51910.49870.85821.6396-0.0299-0.28240.02160.05680.0871-0.07640.13080.0461-0.05720.0720.0337-0.00060.1629-0.01390.15065.1794-24.080525.8945
90.188-0.0313-0.15370.1474-0.11410.3285-0.0162-0.0184-0.0295-0.0289-0.0056-0.0080.02110.00880.02180.1051-0.0070.00690.10820.00130.1069-11.7574-20.080413.1096
100.06670.0846-0.07710.1408-0.06310.41820.0216-0.01530.01040.0256-0.00840.0637-0.0263-0.047-0.01310.1006-0.00650.00950.1338-0.0140.1048-26.6891-10.775218.786
110.7556-0.321-0.1162.3347-0.78930.3586-0.03350.04830.03550.10950.17830.3141-0.0654-0.152-0.14480.07370.06920.04670.31720.0070.0837-36.6194-12.527525.7792
120.11120.0367-0.08160.2021-0.24950.39080.0186-0.04590.0188-0.01990.005-0.039-0.0410.009-0.02350.1066-0.0110.00850.1153-0.01220.1212-7.2372-9.084910.7373
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 44
2X-RAY DIFFRACTION2A45 - 70
3X-RAY DIFFRACTION3A71 - 176
4X-RAY DIFFRACTION4A177 - 261
5X-RAY DIFFRACTION5A262 - 313
6X-RAY DIFFRACTION6A314 - 321
7X-RAY DIFFRACTION7B3 - 44
8X-RAY DIFFRACTION8B45 - 76
9X-RAY DIFFRACTION9B77 - 194
10X-RAY DIFFRACTION10B195 - 258
11X-RAY DIFFRACTION11B259 - 268
12X-RAY DIFFRACTION12B279 - 321

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