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- PDB-3s1w: Transaldolase variant Lys86Ala from Thermoplasma acidophilum in c... -

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Basic information

Entry
Database: PDB / ID: 3s1w
TitleTransaldolase variant Lys86Ala from Thermoplasma acidophilum in complex with glycerol and citrate
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
CITRATE ANION / Probable transaldolase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 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: Data collection / Category: reflns / Item: _reflns.pdbx_Rsym_value
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_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: Probable transaldolase
B: Probable transaldolase
C: Probable transaldolase
D: Probable transaldolase
E: Probable transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,58815
Polymers122,1825
Non-polymers1,40610
Water13,998777
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)247,17630
Polymers244,36410
Non-polymers2,81220
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area49700 Å2
ΔGint-325 kcal/mol
Surface area71600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.080, 168.670, 97.920
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
11E-661-

HOH

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Components

#1: Protein
Probable transaldolase


Mass: 24436.441 Da / Num. of mol.: 5 / Mutation: K86A
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 777 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
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: Jun 3, 2008 / 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: 1.8→19.74 Å / Num. all: 110627 / Num. obs: 110627 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 30.382 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 25.62
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.90.4593.888248316435199.9
1.9-20.2786.296701813323199.9
2-2.20.14311.61100426199491100
2.2-3.120.05127.6719869039388199.9
3.12-3.580.02551.013618072481100
3.58-4.040.02161.51214994331199.9
4.04-4.50.01968.73136282758199.7
4.5-140.01675.77339447078199.1
14-170.0236.3615775165.8
17-200.0625.1410242170

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3S0C

3s0c


Resolution: 1.8→19.447 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.23 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Phase error: 21.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 5529 5 %RANDOM
Rwork0.1762 ---
obs0.1778 110566 99.79 %-
all-110566 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.274 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso max: 86.98 Å2 / Biso mean: 29.4703 Å2 / Biso min: 10.09 Å2
Baniso -1Baniso -2Baniso -3
1-6.3179 Å2-0 Å2-0 Å2
2---2.641 Å2-0 Å2
3----3.6769 Å2
Refine analyzeLuzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8575 0 95 777 9447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088930
X-RAY DIFFRACTIONf_angle_d1.15112138
X-RAY DIFFRACTIONf_chiral_restr0.0631472
X-RAY DIFFRACTIONf_plane_restr0.0051545
X-RAY DIFFRACTIONf_dihedral_angle_d12.6653342
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 (%)
1.8-1.82050.3461830.288134803663100
1.8205-1.84190.3231830.277434603643100
1.8419-1.86430.32151810.2734503631100
1.8643-1.88790.31311850.247935103695100
1.8879-1.91270.28971820.234934683650100
1.9127-1.93890.24861830.222334613644100
1.9389-1.96650.28451830.209534823665100
1.9665-1.99590.23591840.196135013685100
1.9959-2.0270.25331830.194234783661100
2.027-2.06020.22991840.188934923676100
2.0602-2.09570.21681820.175234613643100
2.0957-2.13380.22371840.172334913675100
2.1338-2.17480.20051840.167734983682100
2.1748-2.21910.21031830.170834733656100
2.2191-2.26730.21971840.173835083692100
2.2673-2.31990.22621840.172934843668100
2.3199-2.37780.20771830.173234843667100
2.3778-2.4420.20791830.17534743657100
2.442-2.51370.2281860.173235273713100
2.5137-2.59470.20121840.170635033687100
2.5947-2.68720.20871840.178135003684100
2.6872-2.79450.20421860.170735223708100
2.7945-2.92130.18711840.162835043688100
2.9213-3.07470.18041850.162235233708100
3.0747-3.26650.22621860.1735253711100
3.2665-3.51740.19091860.174135363722100
3.5174-3.86880.18851860.158135343720100
3.8688-4.42290.16771880.147835643752100
4.4229-5.55080.17471890.164635903779100
5.5508-19.44760.20681870.18933554374196
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)
11.180.0611-0.44250.9753-0.53021.4653-0.04040.2266-0.2412-0.3407-0.0341-0.02460.4022-0.07720.06070.24830.02330.00080.1521-0.08550.15138.554-59.6759-3.2873
21.107-0.3481-0.1731.0570.23170.85310.14040.26430.0968-0.1891-0.1249-0.0787-0.11580.0233-0.01980.18340.04440.02740.1920.03570.123410.1768-24.0302-4.2298
30.7017-0.10890.04820.81190.13050.85520.00530.02020.1444-0.0881-0.0110.025-0.1338-0.06490.00370.1520.03620.00540.09120.02070.1261-16.5965-11.513115.8698
41.20770.81860.26421.1999-0.05340.98790.0423-0.07420.1820.0028-0.02730.2663-0.0674-0.242-0.00070.05420.0065-0.00220.15190.0060.137-34.3913-39.335629.5741
51.0048-0.5033-0.06861.02870.43761.2448-0.00490.0727-0.36540.0406-0.11960.2610.2155-0.26220.10720.1454-0.0538-0.01880.1404-0.05730.2877-18.8017-69.049717.8759
60.28680.16340.08840.3210.38550.66570.1236-0.2113-0.70070.2836-0.19010.35460.6016-0.1164-0.0390.4116-0.0674-0.02450.2018-0.01380.5686-13.794-83.556621.0915
70.7789-0.1851-0.04640.6165-0.24790.18770.01170.554-0.24-0.2463-0.0617-0.24750.32070.3170.08210.33510.11910.07690.3846-0.11450.275123.4179-62.2619-7.7455
80.645-0.3412-0.04110.4737-0.41921.3810.15670.0990.3387-0.1703-0.1653-0.3951-0.39170.1181-0.04360.32990.00710.11480.22060.0980.264318.7716-10.9015-3.8234
91.1247-0.1930.58640.0879-0.1860.7521-0.129-0.10340.4130.04830.1066-0.01-0.5852-0.3420.03570.33260.0985-0.00190.2178-0.02340.2533-21.377-0.886226.0563
100.13190.1667-0.07681.2772-0.20691.83150.0408-0.31760.15830.15930.00320.3972-0.0549-0.7186-0.05040.2168-0.04030.03130.45980.01070.298-42.0106-45.41641.8128
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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