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- PDB-3s1v: Transaldolase from Thermoplasma acidophilum in complex with D-fru... -

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Basic information

Entry
Database: PDB / ID: 3s1v
TitleTransaldolase from Thermoplasma acidophilum in complex with D-fructose 6-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
FRUCTOSE -6-PHOSPHATE / 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 / Derived calculations / Category: reflns / struct_conn
Item: _reflns.pdbx_Rsym_value / _struct_conn.pdbx_leaving_atom_flag
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_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 1.5Oct 30, 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)124,05013
Polymers122,4735
Non-polymers1,5778
Water15,907883
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)248,09926
Polymers244,94510
Non-polymers3,15416
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area49550 Å2
ΔGint-365 kcal/mol
Surface area75540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.617, 172.535, 100.277
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-825-

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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-F6R / FRUCTOSE -6-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 883 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
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: Aug 13, 2009 / 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→19.75 Å / Num. all: 118736 / Num. obs: 118736 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.23 % / Biso Wilson estimate: 30.598 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 20.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.90.5434.391473181764099.9
1.9-20.3466.731186091430899.9
2-2.10.22110.14968521170099.9
2.1-2.20.14913.6981074968499.9
2.2-2.660.09320.42339552819799.9
2.66-3.120.05730.061152881400499.9
3.12-3.580.04636.8162710777499.9
3.58-4.040.04142.7636963464199.8
4.04-4.50.03945.9123543295199.9
4.5-100.03747.8557527170100
10-200.03546.91461966799.1
20-30
30

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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→19.745 Å / Occupancy max: 1 / Occupancy min: 0.14 / SU ML: 0.19 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 0 / Phase error: 21.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 5938 5 %RANDOM
Rwork0.175 ---
obs0.1768 118722 99.9 %-
all-118722 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.192 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 105.37 Å2 / Biso mean: 31.0329 Å2 / Biso min: 11.28 Å2
Baniso -1Baniso -2Baniso -3
1-6.3912 Å2-0 Å2-0 Å2
2---3.4175 Å2-0 Å2
3----2.9736 Å2
Refine analyzeLuzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8595 0 93 883 9571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129029
X-RAY DIFFRACTIONf_angle_d1.27512287
X-RAY DIFFRACTIONf_chiral_restr0.0871487
X-RAY DIFFRACTIONf_plane_restr0.0061553
X-RAY DIFFRACTIONf_dihedral_angle_d13.2583406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.82040.31521960.257437013897
1.8204-1.84180.27191970.234637543951
1.8418-1.86430.26771970.215937363933
1.8643-1.88790.24661960.214537293925
1.8879-1.91270.25691950.207236923887
1.9127-1.93890.26341970.20937473944
1.9389-1.96650.25121970.199537483945
1.9665-1.99590.22721980.194337543952
1.9959-2.0270.23651940.188136913885
2.027-2.06020.25571960.18937343930
2.0602-2.09570.23481970.185937393936
2.0957-2.13380.2271980.181737563954
2.1338-2.17480.2141950.172737063901
2.1748-2.21910.20981980.164537643962
2.2191-2.26730.20171980.163937513949
2.2673-2.31990.21541960.168437333929
2.3199-2.37790.23331970.167337423939
2.3779-2.44210.23921970.169737463943
2.4421-2.51380.2021970.168737453942
2.5138-2.59470.20271990.158437713970
2.5947-2.68730.23171960.17237273923
2.6873-2.79460.22481990.171437863985
2.7946-2.92140.18881990.162837703969
2.9214-3.07490.19241980.168537623960
3.0749-3.26670.19251980.164537803978
3.2667-3.51760.21212000.171337873987
3.5176-3.86920.19212000.158737943994
3.8692-4.42360.16842000.155438194019
4.4236-5.55270.19392030.169838554058
5.5527-19.74580.22452100.203639654175
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)
11.31910.0761-0.46581.0018-0.6741.3585-0.05110.1756-0.2585-0.3065-0.0214-0.03170.3408-0.03260.07150.15870.01020.01150.1001-0.0790.16139.0919-60.904-3.2634
21.1491-0.2337-0.07931.20150.14850.79210.11070.23090.1339-0.1444-0.0832-0.0784-0.14490.0577-0.02950.14560.01970.03130.14890.04270.153710.6049-24.409-4.2367
30.705-0.24090.04650.75640.24260.71310.0040.02930.2398-0.1192-0.0320.0471-0.2506-0.04040.02250.16490.05940.00710.04980.0320.2103-17.1312-11.776216.2598
41.10150.62510.28721.2435-0.02661.00660.0135-0.09990.1782-0.0103-0.03060.3352-0.0787-0.26250.02180.05670.0373-0.00230.16830.00280.2539-35.0874-40.247130.2142
50.7606-0.57240.02671.17660.29991.08150.00910.0064-0.36980.0292-0.1060.32950.1765-0.2480.08880.0623-0.0439-0.02230.1147-0.05520.3549-19.0474-70.622218.1992
60.7229-0.16680.02820.0998-0.1730.7032-0.0057-0.1635-0.80980.17340.0080.40180.4508-0.1445-0.01160.2771-0.0773-0.02950.1642-0.02980.7127-14.4282-85.776821.4021
70.7255-0.077-0.25540.4977-0.14080.6526-0.11020.2363-0.43960.03-0.1758-0.1050.30570.23540.1350.23520.07310.08790.2824-0.09790.373124.2353-63.5921-7.7044
80.5883-0.3198-0.22220.29270.20540.3560.1190.06170.4775-0.07830.0257-0.3214-0.53370.1504-0.14180.3451-0.08470.08810.21120.10280.380319.5908-10.9114-4.1704
90.59660.24650.30640.6074-0.3840.654-0.1386-0.22570.44850.15950.02730.2068-0.5084-0.24460.09650.34340.105-0.00270.1852-0.04910.419-22.1708-0.467926.3928
100.0537-0.1337-0.09351.48360.02241.172-0.1857-0.37210.1660.35350.15740.6975-0.1322-0.85170.02940.15280.00580.05460.4762-0.0010.4476-42.5886-46.611742.8086
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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