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- PDB-3lcr: Thioesterase from Tautomycetin Biosynthhetic Pathway -

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Basic information

Entry
Database: PDB / ID: 3lcr
TitleThioesterase from Tautomycetin Biosynthhetic Pathway
ComponentsTautomycetin biosynthetic PKS
KeywordsHYDROLASE / ALPHA-BETA HYDROLASE / THIOESTERASE / POLYKETIDE SYNTHASE / Phosphopantetheine / Transferase
Function / homology
Function and homology information


: / : / (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / : / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity ...: / : / (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / : / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / hydrolase activity, acting on ester bonds / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / zinc ion binding
Similarity search - Function
Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Quinone oxidoreductase/zeta-crystallin, conserved site / : / Quinone oxidoreductase / zeta-crystallin signature. / Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Polyketide synthase dehydratase N-terminal domain ...Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Quinone oxidoreductase/zeta-crystallin, conserved site / : / Quinone oxidoreductase / zeta-crystallin signature. / Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesStreptomyces sp. CK4412 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2 Å
AuthorsAkey, D.L. / Scaglione, J.B. / Smith, J.L. / Sherman, D.H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Biochemical and structural characterization of the tautomycetin thioesterase: analysis of a stereoselective polyketide hydrolase.
Authors: Scaglione, J.B. / Akey, D.L. / Sullivan, R. / Kittendorf, J.D. / Rath, C.M. / Kim, E.S. / Smith, J.L. / Sherman, D.H.
History
DepositionJan 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Tautomycetin biosynthetic PKS
B: Tautomycetin biosynthetic PKS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3146
Polymers69,0652
Non-polymers2484
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-8 kcal/mol
Surface area23530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.102, 80.183, 64.706
Angle α, β, γ (deg.)90.000, 103.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tautomycetin biosynthetic PKS


Mass: 34532.688 Da / Num. of mol.: 2 / Fragment: UNP residues 7326-7620
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. CK4412 (bacteria) / Gene: tmcB / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A4KCE5, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 1.97 Å3/Da / Density % sol: 37.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100-400 mM Ammonium Formate, 30% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97937,0.97956,0.96112
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2008
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979371
20.979561
30.961121
ReflectionRedundancy: 7.4 % / Av σ(I) over netI: 16.36 / Number: 151609 / Rmerge(I) obs: 0.113 / Χ2: 1.6 / D res high: 2.4 Å / D res low: 50 Å / Num. obs: 20570 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.175099.510.0872.1877.4
4.15.1710010.0811.7187.6
3.584.110010.0961.8147.6
3.263.5810010.121.7067.7
3.023.2610010.1651.6067.7
2.853.0210010.2471.4987.7
2.72.8510010.3461.3977.7
2.592.710010.461.3237.5
2.492.5999.910.5521.3586.9
2.42.4997.610.6171.296
ReflectionResolution: 2→50 Å / Num. all: 36395 / Num. obs: 36028 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Χ2: 1.178 / Net I/σ(I): 16.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3389 / Rsym value: 0.511 / Χ2: 1.794 / % possible all: 94.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→36.3 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.275 / WRfactor Rwork: 0.213 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.831 / SU B: 10.695 / SU ML: 0.132 / SU R Cruickshank DPI: 0.198 / SU Rfree: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.198 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1786 5 %RANDOM
Rwork0.187 ---
all0.189 36395 --
obs0.189 35951 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.92 Å2 / Biso mean: 50.437 Å2 / Biso min: 27.64 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å21.39 Å2
2---0.09 Å2-0 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 2→36.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4185 0 14 218 4417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224282
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.9725818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9885548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0223.128195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25315663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6631542
X-RAY DIFFRACTIONr_chiral_restr0.0790.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213318
X-RAY DIFFRACTIONr_mcbond_it0.8463.52727
X-RAY DIFFRACTIONr_mcangle_it1.45954335
X-RAY DIFFRACTIONr_scbond_it0.9523.51555
X-RAY DIFFRACTIONr_scangle_it1.51551483
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 118 -
Rwork0.288 2297 -
all-2415 -
obs-3389 90.28 %
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)
16.8528-2.64760.80767.8724-1.24885.3729-0.193-0.1603-0.05590.90960.15150.03340.29460.21850.04150.3835-0.03950.13420.1099-0.03490.068215.28138.02117.599
24.36250.7731-2.61141.4569-0.64413.8393-0.42380.4369-0.3815-0.16390.11960.16820.6399-0.52730.30420.2507-0.14580.10450.1501-0.07710.12-10.91639.42222.863
33.82760.3789-0.23531.1068-0.07713.1775-0.20670.23350.2158-0.04190.07040.18250.0193-0.34450.13630.1124-0.02340.02670.1215-0.00930.1066-12.21951.22124.187
44.0823-0.3587-0.87243.51610.64943.9478-0.3391-0.1255-0.12890.062-0.0032-0.0730.55360.16140.34240.18690.00980.11710.12070.02110.08136.2543.25524.777
54.6999-0.2176-0.97482.2306-0.29254.1272-0.3163-0.51020.19380.2410.04860.06360.16070.09720.26770.18250.01730.0620.1196-0.02470.0612-5.3848.46538.444
66.9061-1.81450.98933.59980.10088.84090.10640.28030.19630.2695-0.23250.4460.0092-0.30290.12610.1566-0.0230.10050.1561-0.08050.130713.5939.9984.728
72.2863-0.7351-1.34933.67161.75464.8897-0.1551-0.1214-0.39430.49890.0997-0.27870.58750.01520.05540.1327-0.0114-0.02540.1092-0.01420.188432.75423.256-2.099
82.689-1.3771-0.23465.18910.60795.1310.0982-0.1220.1670.25880.18-1.0014-0.20390.5691-0.27830.0417-0.0478-0.05870.2151-0.08390.353241.78530.218-2.491
93.379-0.5569-1.15093.03380.3644.14730.16480.13360.12540.0225-0.1214-0.043-0.3452-0.5118-0.04330.14460.04830.02690.1649-0.03720.062423.20438.159-2.436
104.0037-1.0744-0.34224.84720.30523.47450.20330.42540.2355-0.6893-0.0445-0.747-0.5526-0.0021-0.15880.1895-0.01360.14680.1364-0.02530.155835.91836.424-16.208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 32
2X-RAY DIFFRACTION2A33 - 105
3X-RAY DIFFRACTION3A106 - 165
4X-RAY DIFFRACTION4A166 - 213
5X-RAY DIFFRACTION5A214 - 280
6X-RAY DIFFRACTION6B3 - 32
7X-RAY DIFFRACTION7B33 - 105
8X-RAY DIFFRACTION8B106 - 165
9X-RAY DIFFRACTION9B166 - 213
10X-RAY DIFFRACTION10B214 - 280

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