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- PDB-1mo2: Thioesterase Domain from 6-Deoxyerythronolide Synthase (DEBS TE),... -

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Basic information

Entry
Database: PDB / ID: 1mo2
TitleThioesterase Domain from 6-Deoxyerythronolide Synthase (DEBS TE), pH 8.5
ComponentsErythronolide synthase, modules 5 and 6
KeywordsTRANSFERASE / Thioesterase / Polyketide Synthase / open substrate channel / TE / PKS / alpha beta hydrolase / 6-deoxyerythronolide / picromycin / pikromycin / erythromycin
Function / homology
Function and homology information


6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase, docking domain superfmaily / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Polyketide synthase, ketoreductase domain / KR domain ...Polyketide synthase, docking domain superfmaily / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / 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 / 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
6-deoxyerythronolide-B synthase EryA3, modules 5 and 6
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTsai, S.-C. / Lu, H. / Cane, D.E. / Khosla, C. / Stroud, R.M.
CitationJournal: Biochemistry / Year: 2002
Title: Insights into channel architecture and substrate specificity from crystal structures of two macrocycle-forming thioesterases of modular polyketide synthases
Authors: Tsai, S.-C. / Lu, H. / Cane, D.E. / Khosla, C. / Stroud, R.M.
History
DepositionSep 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Erythronolide synthase, modules 5 and 6
B: Erythronolide synthase, modules 5 and 6


Theoretical massNumber of molelcules
Total (without water)62,5682
Polymers62,5682
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.500, 102.500, 156.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Erythronolide synthase, modules 5 and 6 / / E.C.2.3.1.94 / 6-deoxyerythronolide B synthase III / DEBS 3 / DEBS TE / erythronolide synthase III


Mass: 31283.898 Da / Num. of mol.: 2 / Fragment: Thioesterase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: ERYA / Plasmid: pET21c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q03133, 6-deoxyerythronolide-B synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2

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Sample preparation

CrystalDensity Matthews: 6 Å3/Da / Density % sol: 79.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 400, bicine, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMBicine1reservoirpH8.5
22 mMdithiothreitol1reservoir
3100 mM1reservoirMgCl2
410 mg/mlprotein1drop
520 mMHEPES1droppH7.5
62 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 1999
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 26440 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 13.2 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 9.7
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.7 / % possible all: 100
Reflection
*PLUS
Num. measured all: 350978
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.51

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Processing

Software
NameVersionClassification
REFMAC5.1refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KEZ

1kez


Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.855 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28663 1223 5.1 %RANDOM
Rwork0.24215 ---
all0.2595 26614 --
obs0.24447 22595 89.6 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.64 Å2
Baniso -1Baniso -2Baniso -3
1-4.4 Å20 Å20 Å2
2---1.03 Å20 Å2
3----3.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 0 0 56 3832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0430.0213880
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.5621.9495304
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.5975498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.240.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023058
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3360.22049
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.2179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.7480.2326
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.570.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.3181.52494
X-RAY DIFFRACTIONr_mcangle_it2.4723984
X-RAY DIFFRACTIONr_scbond_it4.18331386
X-RAY DIFFRACTIONr_scangle_it6.9834.51320
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.393 93
Rwork0.279 1531
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)
11.97960.5264-0.31244.0227-3.7018.09570.1379-0.28480.19260.65580.00780.1722-0.7097-0.0596-0.14570.2426-0.0073-0.01760.0783-0.04910.16281.237950.743263.4611
22.9896-0.38860.14945.2681-0.83596.53890.0683-0.1288-0.42950.1066-0.0219-0.65990.90771.3865-0.04640.27920.13460.0090.38170.03120.3017.504639.522362.0341
313.4036-0.3289-2.405414.09930.773811.4652-0.8356-0.6464-2.31-1.97770.6412-1.23210.92341.69240.19440.4539-0.04860.15650.3279-0.02190.39036.524837.272846.4705
48.0159-1.6598-1.07148.9776-3.10287.25550.3739-0.38910.5271-0.7895-0.6408-0.88960.58680.98430.26680.33980.06410.0910.13330.05940.102312.767350.904643.2633
53.3949-0.13362.24412.42450.27266.1430.11710.20690.0802-0.49220.054-0.12210.17750.0338-0.17110.02670.03270.05090.16330.02690.107224.851332.308598.4186
67.72371.26523.21583.61710.29437.7213-0.1019-0.41870.3179-0.60520.21331.2628-0.41-1.9267-0.11140.29710.1382-0.0030.5326-0.05510.338512.30335.217199.5533
710.83757.4091-4.58285.07282.657413.32630.4684-0.64680.90590.3249-0.42652.6659-0.817-2.1137-0.04190.28920.0210.10690.7483-0.02280.629410.081633.7765115.0855
86.8040.02511.25897.80342.68783.084-0.1319-0.56680.9318-0.0126-0.40.0956-0.4596-0.97970.53190.04970.04560.06950.3977-0.08760.269521.368343.5914118.4553
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA26 - 16026 - 160
2X-RAY DIFFRACTION2AA161 - 220161 - 220
3X-RAY DIFFRACTION3AA221 - 250221 - 250
4X-RAY DIFFRACTION4AA251 - 280251 - 280
5X-RAY DIFFRACTION5BB26 - 16026 - 160
6X-RAY DIFFRACTION6BB161 - 220161 - 220
7X-RAY DIFFRACTION7BB221 - 250221 - 250
8X-RAY DIFFRACTION8BB251 - 280251 - 280
Refinement
*PLUS
Highest resolution: 3 Å / σ(F): 0 / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.006
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.67

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