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- PDB-3s1u: Transaldolase from Thermoplasma acidophilum in complex with D-ery... -

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Basic information

Entry
Database: PDB / ID: 3s1u
TitleTransaldolase from Thermoplasma acidophilum in complex with D-erythrose 4-phosphate
ComponentsProbable transaldolase
KeywordsTRANSFERASE / ALPHA-BETA BARREL / DOMAIN SWAPPING / PROTEIN DYNAMICS / CONFORMATIONAL SELECTION
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
ERYTHOSE-4-PHOSPHATE / Probable transaldolase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 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 1.2Oct 5, 2011Group: Database references
Revision 1.3Sep 4, 2019Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms / reflns / Item: _reflns.pdbx_Rsym_value
Revision 1.4Sep 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_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

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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)123,50911
Polymers122,4735
Non-polymers1,0366
Water11,620645
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)247,01722
Polymers244,94510
Non-polymers2,07212
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area44650 Å2
ΔGint-301 kcal/mol
Surface area75450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.200, 171.400, 99.100
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-224-

CL

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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: Sugar
ChemComp-E4P / ERYTHOSE-4-PHOSPHATE


Type: saccharide / Mass: 200.084 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H9O7P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.13 %
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: Dec 4, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.9→19.901 Å / Num. all: 99730 / Num. obs: 99730 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.52 % / Biso Wilson estimate: 34.677 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 31.72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-20.4494.9710621114103100
2-2.10.2698.178752011595100
2.1-2.20.17811.9872036953399.9
2.2-2.30.13615.5460140795599.9
2.3-2.750.0824.591764382330899.9
2.75-3.20.03944.95910091202999.9
3.2-3.650.02663.7751664685499.9
3.65-4.10.02277.3531362419499.9
4.1-4.550.01985.99202392725100
4.55-100.01986.9549574679599.7
10-200.01695.1412363995.5
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: 1.9→19.852 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8648 / SU ML: 0.23 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 0 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 4988 5 %RANDOM
Rwork0.1747 ---
obs0.1759 99704 99.83 %-
all-99704 --
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.312 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 152.93 Å2 / Biso mean: 36.863 Å2 / Biso min: 13.77 Å2
Baniso -1Baniso -2Baniso -3
1-8.4819 Å2-0 Å2-0 Å2
2---4.1942 Å2-0 Å2
3----4.2877 Å2
Refine analyzeLuzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8473 0 61 645 9179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078789
X-RAY DIFFRACTIONf_angle_d1.00811946
X-RAY DIFFRACTIONf_chiral_restr0.0651454
X-RAY DIFFRACTIONf_plane_restr0.0051507
X-RAY DIFFRACTIONf_dihedral_angle_d15.5973274
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 (%)
1.9-1.91660.23791650.21653114327999
1.9166-1.93910.261660.207731193285100
1.9391-1.96270.26041630.213731213284100
1.9627-1.98760.25031660.203231713337100
1.9876-2.01370.22051650.198130933258100
2.0137-2.04120.23491630.194531383301100
2.0412-2.07040.22571650.183531453310100
2.0704-2.10130.23461650.187531283293100
2.1013-2.1340.21041650.179331403305100
2.134-2.1690.24041670.176131283295100
2.169-2.20630.21251620.167231243286100
2.2063-2.24640.22911680.169531733341100
2.2464-2.28960.21981650.171931263291100
2.2896-2.33620.22951640.174331213285100
2.3362-2.38690.221660.174931603326100
2.3869-2.44240.21041650.171531363301100
2.4424-2.50330.21131670.171431593326100
2.5033-2.57090.21391640.171431333297100
2.5709-2.64640.21141670.173331673334100
2.6464-2.73160.22611650.17931293294100
2.7316-2.82890.19631680.173131753343100
2.8289-2.94190.19341660.166231543320100
2.9419-3.07530.17231660.171931823348100
3.0753-3.23680.18481670.167731583325100
3.2368-3.43860.1911680.161731973365100
3.4386-3.70250.15641670.157231643331100
3.7025-4.07220.17681690.152432023371100
4.0722-4.65480.15591680.140532063374100
4.6548-5.83970.17381720.180632513423100
5.8397-19.85330.19841740.19153302347699
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)
11.450.2727-0.91261.0946-0.67492.7177-0.20330.2274-0.3296-0.23570.0029-0.07320.5637-0.11260.18750.2577-0.00950.06110.1846-0.1040.24358.087-60.8898-3.8089
21.2088-0.4364-0.06221.80080.25380.74020.12310.24140.0723-0.4493-0.1478-0.1036-0.17910.01120.0010.31630.04970.03190.23230.01550.144810.2797-24.259-4.439
30.85150.0428-0.16990.96820.05780.71140.07790.07350.0895-0.1405-0.01730.0408-0.1579-0.0656-0.05360.19880.06370.00860.14270.02610.1107-16.9242-11.729315.9691
40.97311.07210.24051.67220.04360.93840.0362-0.09410.13390.0022-0.06170.3104-0.0223-0.26320.03380.1103-0.0113-0.01110.2842-0.01410.2363-35.1524-39.531729.335
51.0105-0.649-0.64041.05540.33561.6392-0.21290.1571-0.47320.0759-0.07060.26820.4972-0.3270.25530.3149-0.14260.08340.2327-0.10560.4394-19.6039-69.874717.43
60.02830.02430.0260.019-0.0390.1426-0.1084-0.0697-0.3450.2366-0.20040.52540.6221-0.27010.14010.6512-0.06120.2040.3799-0.01030.7443-12.5516-84.11122.6157
70.9353-0.5821-0.43060.52950.13470.3365-0.14110.0879-0.559-0.232-0.1222-0.0140.3240.44660.22850.38540.14120.07860.3641-0.0850.476124.4441-62.5361-5.7039
80.49610.00080.05710.60710.13510.68090.12710.05210.0835-0.3636-0.1579-0.4026-0.61960.1985-0.05540.5082-0.01470.12860.2560.0610.238219.156-10.7537-4.5538
90.4134-0.0736-0.02410.5669-0.13770.29620.0913-0.14440.2210.3194-0.03270.4009-0.6361-0.25530.00620.42660.14090.02370.2612-0.04010.3009-22.1773-0.500626.055
100.23550.2078-0.18870.3521-0.02030.50820.0389-0.06210.10950.2887-0.08890.36610.0366-0.6388-0.0210.3663-0.08870.05460.5690.0220.3715-40.479-46.262943.7997
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:198)A1 - 198
2X-RAY DIFFRACTION2CHAIN B AND (RESID 1:198)B1 - 198
3X-RAY DIFFRACTION3CHAIN C AND (RESID 1:198)C1 - 198
4X-RAY DIFFRACTION4CHAIN D AND (RESID 1:198)D1 - 198
5X-RAY DIFFRACTION5CHAIN E AND (RESID 1:198)E1 - 198
6X-RAY DIFFRACTION6CHAIN A AND (RESID 199:230)A199 - 230
7X-RAY DIFFRACTION7CHAIN B AND (RESID 199:230)B199 - 230
8X-RAY DIFFRACTION8CHAIN C AND (RESID 199:230)C199 - 230
9X-RAY DIFFRACTION9CHAIN D AND (RESID 199:230)D199 - 230
10X-RAY DIFFRACTION10CHAIN E AND (RESID 199:230)E199 - 230

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