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- PDB-5bp2: Dehydratase domain (DH) of a mycocerosic acid synthase-like (MAS-... -

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Basic information

Entry
Database: PDB / ID: 5bp2
TitleDehydratase domain (DH) of a mycocerosic acid synthase-like (MAS-like) PKS, crystal form 1
ComponentsMycocerosic acid synthase-like polyketide synthase
KeywordsLYASE / PKS / dehydratase / DH / polyketide
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / secondary metabolite biosynthetic process / 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 / cytoplasm
Similarity search - Function
Polyketide synthase dehydratase / Zinc-binding dehydrogenase / : / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain ...Polyketide synthase dehydratase / Zinc-binding dehydrogenase / : / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / 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 / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / 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: 1.75 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)131,14447
Polymers128,3484
Non-polymers2,79643
Water13,295738
1
A: Mycocerosic acid synthase-like polyketide synthase
hetero molecules

C: Mycocerosic acid synthase-like polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,95129
Polymers64,1742
Non-polymers1,77727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area6950 Å2
ΔGint10 kcal/mol
Surface area23470 Å2
MethodPISA
2
D: Mycocerosic acid synthase-like polyketide synthase
hetero molecules

B: Mycocerosic acid synthase-like polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,19318
Polymers64,1742
Non-polymers1,01916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_443-x-1,y-1/2,-z-21
Buried area4510 Å2
ΔGint-16 kcal/mol
Surface area23290 Å2
MethodPISA
3
C: Mycocerosic acid synthase-like polyketide synthase
hetero molecules

A: Mycocerosic acid synthase-like polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,95129
Polymers64,1742
Non-polymers1,77727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_444-x-1,y-1/2,-z-11
Buried area6950 Å2
ΔGint10 kcal/mol
Surface area23470 Å2
MethodPISA
4
B: Mycocerosic acid synthase-like polyketide synthase
hetero molecules

D: Mycocerosic acid synthase-like polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,19318
Polymers64,1742
Non-polymers1,01916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_453-x-1,y+1/2,-z-21
Buried area4510 Å2
ΔGint-16 kcal/mol
Surface area23290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.650, 162.400, 66.620
Angle α, β, γ (deg.)90.00, 91.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 32086.957 Da / Num. of mol.: 4 / 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

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Non-polymers , 6 types, 781 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 738 / 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: 47.39 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystallization condition: 25 % (w/v) PEG 3350 0.2 M MgCl2 0.1 M BIS-TRIS 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 % ...Details: Crystallization condition: 25 % (w/v) PEG 3350 0.2 M MgCl2 0.1 M BIS-TRIS 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: 0.99987 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.75→66.6 Å / Num. obs: 123118 / % possible obs: 96.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 51.34 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 12.32
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 3.8 % / % possible all: 91.6

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kg9

3kg9


Resolution: 1.75→66.6 Å / Cor.coef. Fo:Fc: 0.9615 / Cor.coef. Fo:Fc free: 0.9544 / SU R Cruickshank DPI: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.11 / SU Rfree Blow DPI: 0.1 / SU Rfree Cruickshank DPI: 0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2032 2012 1.63 %RANDOM
Rwork0.1826 ---
obs0.1829 123105 96.9 %-
Displacement parametersBiso mean: 57.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.6903 Å20 Å2-0.1453 Å2
2--5.4014 Å20 Å2
3----8.0917 Å2
Refine analyzeLuzzati coordinate error obs: 0.222 Å
Refinement stepCycle: 1 / Resolution: 1.75→66.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8723 0 176 738 9637
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0117865HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.132273HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4982SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes189HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2771HARMONIC5
X-RAY DIFFRACTIONt_it17865HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.93
X-RAY DIFFRACTIONt_other_torsion2.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1155SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact20033SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2679 145 1.67 %
Rwork0.2375 8554 -
all0.238 8699 -
obs--93.07 %
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)
11.00890.4058-0.03643.0360.20270.92560.0366-0.03890.20110.4847-0.02150.2816-0.2037-0.0224-0.01510.0651-0.00610.0072-0.14870.0139-0.085-15.755325.2552-27.0769
20.8964-0.5062-1.02484.88641.98612.2930.09870.00250.04730.50630.0129-0.2508-0.05130.0579-0.11160.010.0037-0.1076-0.09720.0453-0.1258-6.627112.4201-30.4268
30.93450.1712-0.11141.87750.24380.9771-0.0110.05990.00330.128-0.01850.1153-0.1008-0.07910.0294-0.0217-0.0128-0.0215-0.03810.0155-0.0566-16.11746.1758-35.8179
41.22110.0251-0.08172.2521-0.14230.73240.0463-0.01650.03550.2261-0.04770.0267-0.12790.08250.00140.006-0.0134-0.0374-0.0490.0179-0.0517-8.7056.7102-33.3433
50.22830.99280.28324.31140.50550.66730.0465-0.05550.11690.1303-0.0447-0.0562-0.11570.0128-0.0019-0.01660.0008-0.0276-0.11910.0095-0.0389-45.349437.2802-59.2759
60.6846-1.3826-0.73115.18161.78221.70930.08170.09160.02680.2530.0074-0.4437-0.00850.0603-0.0892-0.0989-0.0125-0.0744-0.09070.00270.0131-36.261524.1117-61.3906
71.7013-0.438-0.32371.93760.32760.9960.07210.1753-0.1002-0.1101-0.054-0.0149-0.08890.0017-0.018-0.04160.0085-0.0338-0.06880.0147-0.0303-47.507216.5105-67.2424
82.4115-0.4795-0.08844.0310.53121.52230.05380.00090.07050.15820.0184-0.3708-0.07590.1302-0.0723-0.0696-0.0073-0.0536-0.12240.01320.0142-37.274719.4807-62.446
90.7517-0.3404-0.14922.75140.240.8243-0.05550.0064-0.2031-0.17570.00510.01280.20430.01370.05040.00040.00920.0207-0.11610.0154-0.0315-45.534-29.7002-40.4979
101.18261.38380.78395.00722.08912.16640.0786-0.0963-0.0331-0.27410.0003-0.29540.02190.076-0.0788-0.07570.01910.0462-0.07540.0221-0.0572-36.5056-16.3817-38.2477
111.53630.1544-0.01520.94460.0970.63220.0265-0.20930.1683-0.0069-0.02110.03450.03270.001-0.0055-0.0448-0.00810.0012-0.02790.0061-0.0018-47.4416-8.8323-32.3879
122.62120.37380.01713.32580.0510.71480.0504-0.0643-0.0081-0.18650.0106-0.10750.06340.0513-0.061-0.06630.00040.0232-0.07850.0116-0.0402-37.4893-11.3556-36.5759
130.5476-0.38150.06422.49560.3310.7077-0.0131-0.0505-0.1652-0.0452-0.01790.07430.1775-0.03180.031-0.0024-0.00330.0266-0.06140.0145-0.0484-15.8185-19.4004-69.6551
142.8365-0.1465-0.36162.95260.20461.3509-0.01040.0866-0.1521-0.3409-0.02480.04340.15810.04580.03530.02880.0130.0282-0.06490.0111-0.1161-14.1068-15.962-76.5119
150.91650.67151.23173.52761.81232.39640.08410.0489-0.0332-0.23850.0442-0.3221-0.00740.0509-0.1283-0.0517-0.01180.0739-0.03670.0276-0.0648-6.3373-4.5212-69.2751
161.0910.28760.1711.66420.60931.0897-0.0243-0.09810.1096-0.0174-0.08910.118-0.0365-0.14390.1134-0.04190.021-0.0008-0.0217-0.0044-0.043-17.39032.3174-63.2114
171.45370.52170.4382.14080.43892.422-0.03840.02070.0095-0.1515-0.0052-0.0857-0.0951-0.04140.0436-0.03120.01160.0304-0.05540.0137-0.0489-7.72010.1863-67.1072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|895 - A|1002 }
2X-RAY DIFFRACTION2{ A|1003 - A|1036 }
3X-RAY DIFFRACTION3{ A|1037 - A|1130 }
4X-RAY DIFFRACTION4{ A|1131 - A|1179 }
5X-RAY DIFFRACTION5{ B|894 - B|1002 }
6X-RAY DIFFRACTION6{ B|1003 - B|1036 }
7X-RAY DIFFRACTION7{ B|1037 - B|1124 }
8X-RAY DIFFRACTION8{ B|1125 - B|1177 }
9X-RAY DIFFRACTION9{ C|894 - C|1002 }
10X-RAY DIFFRACTION10{ C|1003 - C|1036 }
11X-RAY DIFFRACTION11{ C|1037 - C|1125 }
12X-RAY DIFFRACTION12{ C|1126 - C|1178 }
13X-RAY DIFFRACTION13{ D|895 - D|959 }
14X-RAY DIFFRACTION14{ D|960 - D|1002 }
15X-RAY DIFFRACTION15{ D|1003 - D|1036 }
16X-RAY DIFFRACTION16{ D|1037 - D|1125 }
17X-RAY DIFFRACTION17{ D|1126 - D|1181 }

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