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- PDB-4e0c: 1.8 Angstrom Resolution Crystal Structure of Transaldolase from F... -

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Basic information

Entry
Database: PDB / ID: 4e0c
Title1.8 Angstrom Resolution Crystal Structure of Transaldolase from Francisella tularensis (phosphate-free)
ComponentsTransaldolase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / 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
ACETATE ION / Transaldolase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLight, S.H. / Minasov, G. / Halavaty, A.S. / 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
DepositionMar 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Sep 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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)77,0354
Polymers76,9522
Non-polymers832
Water13,565753
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-13 kcal/mol
Surface area26120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.761, 87.019, 140.688
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transaldolase /


Mass: 38476.074 Da / Num. of mol.: 2 / Fragment: Transaldolase (TalA)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: FTT_1093c, talA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5NFX0, transaldolase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 753 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 11.2 mg/ml, 0.5 M sodium chloride, 0.01 M Tris-HCl (pH 8.3), Screen: Pegs G1 (Qiagen), 0.2 M magnesium chloride, 20% (w/v) Peg 3350, 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: Feb 9, 2012 / 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: 62204 / Num. obs: 62204 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 20.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 4 / % possible all: 99.4

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Processing

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

3igx


Resolution: 1.8→29.59 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.961 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18917 3147 5.1 %RANDOM
Rwork0.15062 ---
obs0.15254 58978 98.31 %-
all-58978 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.577 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2---0.35 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4872 0 5 753 5630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.025056
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.9756856
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.745656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82726.15213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07315991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1051518
X-RAY DIFFRACTIONr_chiral_restr0.1530.2823
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023662
X-RAY DIFFRACTIONr_gen_planes_other
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: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 215 -
Rwork0.191 3922 -
obs--96.39 %
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)
12.7994-1.5542-0.46062.07070.69931.4858-0.1335-0.1808-0.24430.20240.06730.08420.24830.00340.06620.09570.00660.01720.05370.03450.09022.1274-23.957715.0799
213.22076.0334-3.32666.1333-1.22536.2124-0.08-0.3965-0.65950.047-0.1225-0.11180.8555-0.30350.20250.1894-0.0266-0.0060.14140.02480.1385-17.6739-18.198215.3316
36.4496-2.47270.01512.0159-0.49192.7849-0.2039-0.37880.03430.3060.24770.0966-0.2225-0.5595-0.04380.13490.05270.02560.22580.01740.0726-17.0619-9.211425.471
40.813-0.20930.16171.0372-0.46441.2588-0.0431-0.07920.07650.11190.0304-0.0361-0.1545-0.03980.01260.07610.0042-0.01330.0554-0.00590.0714-4.6303-0.846216.4668
50.976-0.34820.01711.87420.14581.27090.04310.095-0.0102-0.2129-0.04-0.06310.04330.1162-0.00310.08190.01280.02010.07260.01360.08983.7647-11.60810.5003
64.30230.0882-0.86384.1196-1.00882.29750.02080.0096-0.1323-0.258-0.1286-0.10370.18150.14680.10790.11010.04020.00490.05730.00430.06386.09-25.88956.0368
70.86090.3378-0.41410.9889-0.65032.2337-0.02250.02110.0323-0.01380.06160.01240.0664-0.0837-0.03920.06830.0248-0.01470.05290.00620.0878-8.7364-0.83822.053
842.68331.6804-10.06912.9826-0.991129.8961-0.4535-0.2347-0.78550.3870.13730.75380.0768-2.53490.31620.1020.01290.05410.51940.09190.176-29.3887-8.988819.7593
95.08530.24-0.80681.26190.49472.12130.02640.43240.232-0.1901-0.02940.0477-0.211-0.12870.00290.09690.0211-0.0120.12350.02830.0682-24.765220.3967-30.2175
104.0288-1.57790.38651.87280.19120.4853-0.01830.34610.1283-0.001-0.0817-0.28260.02190.10420.10010.06270.01650.01990.14220.02520.1115-9.918117.1933-26.429
113.17671.32822.25862.54032.04824.5911-0.03060.22420.2714-0.1271-0.0067-0.1937-0.20930.1360.03730.0913-0.02490.03710.17110.04820.20545.788325.4988-25.3542
121.03910.02450.30040.65170.00871.1422-0.02180.07550.11860.0146-0.0135-0.0753-0.11430.06310.03530.04740.0030.00330.0640.00560.0921-9.560523.9193-13.581
130.39470.18790.12612.53710.62460.846-0.0175-0.0184-0.0392-0.03420.04720.04460.0915-0.0388-0.02970.0540.0021-0.01030.09290.00210.0673-19.8587.333-12.3236
140.6298-0.1017-0.0550.6057-0.1091.5820.02990.0601-0.0344-0.07420.00260.06460.1182-0.1313-0.03250.0509-0.0031-0.01430.0994-0.00550.078-27.114910.8763-19.3201
156.13350.305711.17770.95232.967626.62910.001-0.3015-0.23160.14560.02290.17120.3694-0.4708-0.02390.1209-0.00190.02540.20320.00250.1444-35.692513.3569-19.5589
160.88860.2517-0.31470.7497-0.61741.4318-0.01390.0684-0.0118-0.03410.0131-0.1040.09740.07640.00090.05490.0209-0.00560.067-0.00960.0838-6.71719.0282-11.6652
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 35
2X-RAY DIFFRACTION2A36 - 50
3X-RAY DIFFRACTION3A51 - 96
4X-RAY DIFFRACTION4A97 - 166
5X-RAY DIFFRACTION5A167 - 247
6X-RAY DIFFRACTION6A248 - 269
7X-RAY DIFFRACTION7A278 - 316
8X-RAY DIFFRACTION8A317 - 321
9X-RAY DIFFRACTION9B2 - 29
10X-RAY DIFFRACTION10B30 - 46
11X-RAY DIFFRACTION11B47 - 77
12X-RAY DIFFRACTION12B78 - 166
13X-RAY DIFFRACTION13B167 - 195
14X-RAY DIFFRACTION14B196 - 260
15X-RAY DIFFRACTION15B261 - 279
16X-RAY DIFFRACTION16B280 - 321

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