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- PDB-3s1x: Transaldolase from Thermoplasma acidophilum in complex with D-sed... -

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Basic information

Entry
Database: PDB / ID: 3s1x
TitleTransaldolase from Thermoplasma acidophilum in complex with D-sedoheptulose 7-phosphate Schiff-base intermediate
ComponentsProbable transaldolase
KeywordsTRANSFERASE / ALPHA-BETA BARREL / CONFORMATIONAL SELECTION / DOMAIN SWAPPING
Function / homology
Function and homology information


transaldolase / transaldolase activity / aldehyde-lyase activity / pentose-phosphate shunt / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Transaldolase type 3B, putative / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / 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 ...Transaldolase type 3B, putative / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / 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 / Probable transaldolase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsLehwess-Litzmann, A. / Neumann, P. / Parthier, C. / Tittmann, K.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: Twisted Schiff base intermediates and substrate locale revise transaldolase mechanism.
Authors: Lehwess-Litzmann, A. / Neumann, P. / Parthier, C. / Ludtke, S. / Golbik, R. / Ficner, R. / Tittmann, K.
History
DepositionMay 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Database references
Revision 1.2Sep 14, 2011Group: Non-polymer description
Revision 1.3Oct 5, 2011Group: Database references
Revision 1.4Sep 4, 2019Group: Data collection / Derived calculations / Category: reflns / struct_conn
Item: _reflns.pdbx_Rsym_value / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable transaldolase
B: Probable transaldolase
C: Probable transaldolase
D: Probable transaldolase
E: Probable transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,92410
Polymers122,4735
Non-polymers1,4515
Water21,7981210
1
A: Probable transaldolase
B: Probable transaldolase
C: Probable transaldolase
D: Probable transaldolase
E: Probable transaldolase
hetero molecules

A: Probable transaldolase
B: Probable transaldolase
C: Probable transaldolase
D: Probable transaldolase
E: Probable transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,84720
Polymers244,94510
Non-polymers2,90210
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area47650 Å2
ΔGint-283 kcal/mol
Surface area77000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.579, 172.802, 100.362
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-782-

HOH

21C-949-

HOH

31C-1225-

HOH

41E-386-

HOH

51E-647-

HOH

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Components

#1: Protein
Probable transaldolase


Mass: 24494.545 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic)
Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165
Gene: Ta0616, tal / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q9HKI3, transaldolase
#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.: 5 / Source method: obtained synthetically / Formula: C7H15O10P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1210 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE GENE WAS CLONED FROM AUTHENTIC DNA DERIVED FROM WILD-TYPE THERMOPLASMA ACIDOPHILUM.

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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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 4.5
Details: PEG 6000, GOL, pH 4.5, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 11, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.65→19.916 Å / Num. all: 152106 / Num. obs: 152106 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 31.346 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 26.93
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.65-1.750.5092.82902002422398
1.75-1.850.3034.66722261939998.3
1.85-1.950.1797.75582531566998.6
1.95-2.050.10812.25475481277098.5
2.05-2.540.04725.451400353771399
2.54-3.030.02445.32637101732099.3
3.03-3.520.01761.8332911899299
3.52-4.010.01475.2918857516498.9
4.01-4.50.01386.4711586316498.9
4.5-100.01290.1925609708098.5
10-200.01193.94203561290.9
20-30
30

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3S0C

3s0c


Resolution: 1.65→19.916 Å / Occupancy max: 1 / Occupancy min: 0.04 / SU ML: 0.21 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Phase error: 20.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 7607 5 %RANDOM
Rwork0.1674 ---
obs0.1689 152094 98.63 %-
all-152094 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.375 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 94.65 Å2 / Biso mean: 31.8447 Å2 / Biso min: 12.71 Å2
Baniso -1Baniso -2Baniso -3
1-4.9311 Å2-0 Å2-0 Å2
2---2.1296 Å2-0 Å2
3----2.8015 Å2
Refine analyzeLuzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.65→19.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8595 0 85 1210 9890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099042
X-RAY DIFFRACTIONf_angle_d1.33512322
X-RAY DIFFRACTIONf_chiral_restr0.0761497
X-RAY DIFFRACTIONf_plane_restr0.0061556
X-RAY DIFFRACTIONf_dihedral_angle_d16.6733376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.66870.32292490.26694697494698
1.6687-1.68840.28962480.25174726497498
1.6884-1.70890.24712530.2324793504698
1.7089-1.73060.25692490.22814730497998
1.7306-1.75330.24222500.22154764501498
1.7533-1.77730.27212510.21684752500399
1.7773-1.80270.26392500.21644754500498
1.8027-1.82960.24262510.20384778502998
1.8296-1.85820.21042510.1944768501998
1.8582-1.88860.24882520.19534782503499
1.8886-1.92110.2392520.18274789504199
1.9211-1.95610.21972520.18194783503599
1.9561-1.99360.21032520.18274796504899
1.9936-2.03430.23512530.17964804505799
2.0343-2.07850.20042530.17544804505799
2.0785-2.12680.22782520.17044794504699
2.1268-2.17990.21822540.16924815506999
2.1799-2.23880.21722540.1564834508899
2.2388-2.30460.20082540.16114819507399
2.3046-2.37880.19932540.16134840509499
2.3788-2.46370.19692540.16054812506699
2.4637-2.56210.18012570.15854882513999
2.5621-2.67850.21612540.15854828508299
2.6785-2.81930.19192560.1644869512599
2.8193-2.99540.19562570.15784876513399
2.9954-3.22580.17482560.15664873512999
3.2258-3.54880.19192580.15544893515199
3.5488-4.05850.15692570.13714892514999
4.0585-5.09910.15572600.12894944520499
5.0991-19.91780.17972640.17284996526097
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)
10.37420.1822-0.0220.1345-0.0180.7066-0.20020.1917-0.33280.13830.1057-0.02260.6394-0.17350.08760.3928-0.03140.04050.2172-0.09370.26666.4587-71.7563-1.5941
20.3018-0.10950.17870.31340.02950.19920.04110.1525-0.0425-0.1546-0.0771-0.0715-0.00360.20870.03780.226-0.01140.07260.34160.03480.202717.6629-30.6862-9.961
30.4776-0.0760.35890.0673-0.14860.37840.08710.16950.35760.0191-0.1069-0.3107-0.2810.05490.01430.39960.08560.07890.16990.11180.3501-10.2018-5.062310.5787
40.66570.04930.33220.14640.13030.2843-0.0107-0.21610.50840.04580.02530.2118-0.2581-0.17960.01880.16960.10230.01030.2554-0.02710.3108-38.3067-29.829632.1336
50.21840.16970.27860.42810.33710.55760.1243-0.33480.01380.2033-0.24190.53690.0215-0.38790.0780.1705-0.07120.01930.3027-0.03590.4161-28.1251-71.071324.6961
60.63150.1191-0.38280.61770.07050.6504-0.2140.4263-0.4748-0.57540.1301-0.03180.5986-0.00990.09590.58020.0330.10450.354-0.19850.368412.0456-75.6608-10.7588
71.72830.06560.08170.8412-0.34830.34070.07720.91780.007-0.4641-0.1074-0.27220.05220.36640.12050.26860.00010.11760.59290.11450.166420.7097-22.1765-17.1513
80.44030.0506-0.00670.4971-0.12950.24510.06990.01350.5314-0.3309-0.0913-0.4081-0.5967-0.14750.04470.66880.0950.00570.13490.04870.3922-17.39893.931610.8245
90.35010.33720.31430.77640.08370.47170.1512-0.5350.43640.1958-0.12070.5435-0.2212-0.49390.03070.21480.13640.00930.501-0.10620.4401-49.0387-32.545135.2144
100.51350.4638-0.56711.3326-0.16121.02170.02860.0092-0.43570.0201-0.09910.55530.2164-0.78350.08580.2565-0.1660.00670.3631-0.01720.5224-30.8702-81.841421.9566
111.0530.1306-0.29861.0899-0.35450.66240.00730.1975-0.0827-0.2371-0.0213-0.02680.10110.01320.0110.17670.01460.00060.2013-0.04260.13479.1854-56.6824-2.1393
120.8656-0.1992-0.00850.92910.08820.73920.07120.19650.1351-0.068-0.0587-0.0221-0.17910.0532-0.01560.20850.00290.02810.19820.03910.15447.3244-23.6223-0.9597
130.3982-0.0452-0.06020.7990.14980.56750.01520.00510.1271-0.0497-0.01730.0689-0.1915-0.06770.00180.23310.06950.01960.14430.02170.1896-18.4764-15.680918.3048
140.46170.17530.01430.6363-0.120.62820.0318-0.0395-0.0181-0.0412-0.00970.0842-0.0169-0.1631-0.02370.10160.0323-0.0040.20330.01440.1622-32.265-43.771828.9931
150.5932-0.3379-0.00420.67240.08780.76310.04340.0593-0.1484-0.0338-0.05720.09730.1097-0.12940.00960.1188-0.0168-0.02940.1523-0.02730.2028-15.3399-69.098516.1978
160.4947-0.17590.0660.3-0.03450.46140.2066-0.212-0.59570.2293-0.1740.29770.4691-0.1311-0.02040.3275-0.0729-0.05170.2119-0.02610.5103-14.5514-86.335521.249
170.8731-0.2822-0.29670.5527-0.15750.3963-0.060.5218-0.2109-0.1767-0.1625-0.23630.22230.18640.10090.27250.05520.10210.4203-0.10740.270624.2552-64.0699-8.0517
180.54630.2136-0.39080.7801-0.45570.5245-0.00630.20520.3379-0.1317-0.0111-0.2614-0.42160.1186-0.0630.4104-0.10590.07760.29030.12070.301319.6437-11.1308-4.2739
190.1629-0.01190.00450.1897-0.1440.13340.0009-0.1150.3606-0.1024-0.10510.1753-0.4713-0.15740.0830.48610.13370.00390.2484-0.0650.4278-21.8559-0.860726.8018
200.15050.1688-0.13840.4579-0.08880.27950.1164-0.29050.08330.1950.01070.2269-0.0218-0.5603-0.08860.17610.0220.0540.51640.02170.2732-43.1253-46.55142.7415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:33)A1 - 33
2X-RAY DIFFRACTION2CHAIN B AND (RESID 1:33)B1 - 33
3X-RAY DIFFRACTION3CHAIN C AND (RESID 1:33)C1 - 33
4X-RAY DIFFRACTION4CHAIN D AND (RESID 1:33)D1 - 33
5X-RAY DIFFRACTION5CHAIN E AND (RESID 1:33)E1 - 33
6X-RAY DIFFRACTION6CHAIN A AND (RESID 34:55)A34 - 55
7X-RAY DIFFRACTION7CHAIN B AND (RESID 34:55)B34 - 55
8X-RAY DIFFRACTION8CHAIN C AND (RESID 34:55)C34 - 55
9X-RAY DIFFRACTION9CHAIN D AND (RESID 34:55)D34 - 55
10X-RAY DIFFRACTION10CHAIN E AND (RESID 34:55)E34 - 55
11X-RAY DIFFRACTION11CHAIN A AND (RESID 56:198)A56 - 198
12X-RAY DIFFRACTION12CHAIN B AND (RESID 56:198)B56 - 198
13X-RAY DIFFRACTION13CHAIN C AND (RESID 56:198)C56 - 198
14X-RAY DIFFRACTION14CHAIN D AND (RESID 56:198)D56 - 198
15X-RAY DIFFRACTION15CHAIN E AND (RESID 56:198)E56 - 198
16X-RAY DIFFRACTION16CHAIN A AND (RESID 199:230)A199 - 230
17X-RAY DIFFRACTION17CHAIN B AND (RESID 199:230)B199 - 230
18X-RAY DIFFRACTION18CHAIN C AND (RESID 199:230)C199 - 230
19X-RAY DIFFRACTION19CHAIN D AND (RESID 199:230)D199 - 230
20X-RAY DIFFRACTION20CHAIN E AND (RESID 199:230)E199 - 230

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