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- PDB-5bp3: Dehydratase domain (DH) of a mycocerosic acid synthase-like (MAS-... -

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Basic information

Entry
Database: PDB / ID: 5bp3
TitleDehydratase domain (DH) of a mycocerosic acid synthase-like (MAS-like) PKS, crystal form 2
ComponentsMycocerosic acid synthase-like polyketide synthase
KeywordsLYASE / PKS / dehydratase / DH / polyketide
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / oxidoreductase activity / plasma membrane
Similarity search - Function
Polyketide synthase dehydratase / Zinc-binding dehydrogenase / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / : / Polyketide synthase dehydratase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily ...Polyketide synthase dehydratase / Zinc-binding dehydrogenase / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / : / Polyketide synthase dehydratase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Thiol Ester Dehydrase; Chain A / 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 / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / 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 / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Mycocerosic acid synthase-like polyketide synthase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHerbst, D.A. / Jakob, P.R. / Zaehringer, F. / Maier, T.
Funding support Switzerland, 4items
OrganizationGrant numberCountry
Swiss National Science Foundation125357 Switzerland
Swiss National Science Foundation138262 Switzerland
Swiss National Science Foundation159696 Switzerland
Swiss National Science Foundation145023 Switzerland
CitationJournal: Nature / Year: 2016
Title: Mycocerosic acid synthase exemplifies the architecture of reducing polyketide synthases.
Authors: Herbst, D.A. / Jakob, R.P. / Zahringer, F. / Maier, T.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Apr 6, 2016Group: Database references
Revision 1.3Dec 28, 2016Group: Structure summary
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 10, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mycocerosic acid synthase-like polyketide synthase
B: Mycocerosic acid synthase-like polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5468
Polymers64,1742
Non-polymers3726
Water8,953497
1
A: Mycocerosic acid synthase-like polyketide synthase
hetero molecules

B: Mycocerosic acid synthase-like polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5468
Polymers64,1742
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_476x-1/2,-y+5/2,-z+11
Buried area2950 Å2
ΔGint0 kcal/mol
Surface area22740 Å2
MethodPISA
2
B: Mycocerosic acid synthase-like polyketide synthase
hetero molecules

A: Mycocerosic acid synthase-like polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5468
Polymers64,1742
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_576x+1/2,-y+5/2,-z+11
Buried area2950 Å2
ΔGint0 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.060, 162.200, 59.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Components on special symmetry positions
IDModelComponents
11A-1355-

HOH

21A-1550-

HOH

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Components

#1: Protein Mycocerosic acid synthase-like polyketide synthase / MAS-like PKS / Polyketide synthase Pks5


Mass: 32086.957 Da / Num. of mol.: 2 / Fragment: UNP residues 884-1186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Cell line: Mybobacterium / Gene: pks5, MSMEG_4727 / Plasmid: pNIC28-Bsa4
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0R1E8, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystallization condition: 16 % (w/v) PEG 3350 0.25 M disodium malonate 0.1 M BIS-TRIS propane pH 6.5 Protein/buffer: 38 mg/ml protein 0.02 M HEPES pH 7.4 0.25 M NaCl 5 % (v/v) Glycerol 0. ...Details: Crystallization condition: 16 % (w/v) PEG 3350 0.25 M disodium malonate 0.1 M BIS-TRIS propane pH 6.5 Protein/buffer: 38 mg/ml protein 0.02 M HEPES pH 7.4 0.25 M NaCl 5 % (v/v) Glycerol 0.005 M DTT Cryo: 25 % (v/v) Ethylene glycol (final)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→47.99 Å / Num. obs: 115067 / % possible obs: 99.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 30.151 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 19.07
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 6.5 % / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
PHASERphasing
XSCALEVERSION July 4, 2012 BUILT=20131111data scaling
XDSNovember 11, 2013data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BP2

5bp2


Resolution: 1.45→47.968 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1774 2000 1.74 %Random selection
Rwork0.1491 ---
obs0.1496 114809 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.291 Å2
Refinement stepCycle: LAST / Resolution: 1.45→47.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 24 497 4702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114587
X-RAY DIFFRACTIONf_angle_d1.3096298
X-RAY DIFFRACTIONf_dihedral_angle_d11.3841646
X-RAY DIFFRACTIONf_chiral_restr0.074731
X-RAY DIFFRACTIONf_plane_restr0.007842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48630.39881350.33977617X-RAY DIFFRACTION95
1.4863-1.52650.32881410.28917912X-RAY DIFFRACTION98
1.5265-1.57140.27851410.25287940X-RAY DIFFRACTION99
1.5714-1.62210.33111400.23467958X-RAY DIFFRACTION99
1.6221-1.68010.27711420.2148005X-RAY DIFFRACTION99
1.6801-1.74740.22811420.17988037X-RAY DIFFRACTION100
1.7474-1.82690.21821430.16068031X-RAY DIFFRACTION100
1.8269-1.92320.19041440.13868077X-RAY DIFFRACTION100
1.9232-2.04370.1841430.13918073X-RAY DIFFRACTION100
2.0437-2.20150.18081430.12338097X-RAY DIFFRACTION100
2.2015-2.42310.17211440.12178123X-RAY DIFFRACTION100
2.4231-2.77370.15491440.13238171X-RAY DIFFRACTION100
2.7737-3.49440.16091470.13838255X-RAY DIFFRACTION100
3.4944-47.99460.14971510.14598513X-RAY DIFFRACTION100

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