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- PDB-2hg4: Structure of the ketosynthase-acyltransferase didomain of module ... -

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Basic information

Entry
Database: PDB / ID: 2hg4
TitleStructure of the ketosynthase-acyltransferase didomain of module 5 from DEBS.
Components6-Deoxyerythronolide B Synthase
KeywordsTRANSFERASE / ketosynthase / acyltransferase / module 5 / DEBS
Function / homology
Function and homology information


6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #3290 / Polyketide synthase, docking domain superfmaily / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Thioesterase / Thioesterase domain ...Alpha-Beta Plaits - #3290 / Polyketide synthase, docking domain superfmaily / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / PKS_PP_betabranch / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / 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 / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 6-deoxyerythronolide-B synthase EryA3, modules 5 and 6 / EryAIII
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.73 Å
AuthorsTang, Y. / Kim, C.Y. / Mathews, I.I. / Cane, D.E. / Khosla, C.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: The 2.7-A crystal structure of a 194-kDa homodimeric fragment of the 6-deoxyerythronolide B synthase.
Authors: Tang, Y. / Kim, C.Y. / Mathews, I.I. / Cane, D.E. / Khosla, C.
#1: Journal: Biochemistry / Year: 2004
Title: Reconstituting modular activity from separated domains of 6-deoxyerythronolide B synthase.
Authors: Kim, C.Y. / Alekseyev, V.Y. / Chen, A.Y. / Tang, Y. / Cane, D.E. / Khosla, C.
#2: Journal: Science / Year: 1998
Title: Harnessing the biosynthetic code: combinations, permutations, and mutations.
Authors: Cane, D.E. / Walsh, C.T. / Khosla, C.
History
DepositionJun 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-Deoxyerythronolide B Synthase
B: 6-Deoxyerythronolide B Synthase
C: 6-Deoxyerythronolide B Synthase
D: 6-Deoxyerythronolide B Synthase
E: 6-Deoxyerythronolide B Synthase
F: 6-Deoxyerythronolide B Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)588,89722
Polymers587,8866
Non-polymers1,01216
Water5,585310
1
A: 6-Deoxyerythronolide B Synthase
B: 6-Deoxyerythronolide B Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,3087
Polymers195,9622
Non-polymers3465
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-65 kcal/mol
Surface area64740 Å2
MethodPISA, PQS
2
C: 6-Deoxyerythronolide B Synthase
D: 6-Deoxyerythronolide B Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,2477
Polymers195,9622
Non-polymers2855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-64 kcal/mol
Surface area65000 Å2
MethodPISA, PQS
3
E: 6-Deoxyerythronolide B Synthase
F: 6-Deoxyerythronolide B Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,3438
Polymers195,9622
Non-polymers3816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-71 kcal/mol
Surface area63730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)305.258, 150.149, 184.378
Angle α, β, γ (deg.)90.00, 110.03, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRASPAA27 - 45727 - 457
21THRASPBB27 - 45727 - 457
31THRASPCC27 - 45727 - 457
41THRASPDD27 - 45727 - 457
51THRASPEE27 - 45727 - 457
61THRASPFF27 - 45727 - 457
12GLYILEAA466 - 901466 - 901
22GLYILEBB466 - 901466 - 901
32GLYILECC466 - 901466 - 901
42GLYILEDD466 - 901466 - 901
52GLYILEEE466 - 901466 - 901
62GLYILEFF466 - 901466 - 901

NCS ensembles :
ID
1
2
DetailsDimer. Molecules A and B, C and D, E and F form biological dimers.

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Components

#1: Protein
6-Deoxyerythronolide B Synthase / DEBS


Mass: 97980.922 Da / Num. of mol.: 6
Fragment: ketosynthase-acyltransferase didomain of didomain module 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: eryA / Plasmid: pAYC10 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21
References: UniProt: Q5UNP4, UniProt: Q03133*PLUS, 6-deoxyerythronolide-B synthase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000, 0.2M Lithium Sulfate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9392, 0.9793, 0.9789
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 13, 2005 / Details: mirrors
RadiationMonochromator: Single Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.93921
20.97931
30.97891
ReflectionResolution: 2.73→48.17 Å / Num. all: 206652 / Num. obs: 206652 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 57.3 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 8.3
Reflection shellResolution: 2.73→2.88 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.9 / Num. unique all: 30114 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
SHELXphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.73→48.03 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / SU B: 34.897 / SU ML: 0.299 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.607 / ESU R Free: 0.318
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 10395 5 %RANDOM
Rwork0.21612 ---
all0.2181 206602 --
obs0.2181 196207 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-4.51 Å2
2--0.62 Å20 Å2
3----3.53 Å2
Refinement stepCycle: LAST / Resolution: 2.73→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39038 0 54 310 39402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02239848
X-RAY DIFFRACTIONr_bond_other_d0.0010.0236915
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.95754195
X-RAY DIFFRACTIONr_angle_other_deg0.829384883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14755263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49522.3771742
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.575155903
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.08815455
X-RAY DIFFRACTIONr_chiral_restr0.0780.26034
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0246032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028461
X-RAY DIFFRACTIONr_nbd_refined0.2320.29308
X-RAY DIFFRACTIONr_nbd_other0.1820.238594
X-RAY DIFFRACTIONr_nbtor_refined0.1850.219624
X-RAY DIFFRACTIONr_nbtor_other0.0890.225861
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2932
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0760.26
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.250
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.2205
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6061.530548
X-RAY DIFFRACTIONr_mcbond_other0.0931.510844
X-RAY DIFFRACTIONr_mcangle_it0.772241414
X-RAY DIFFRACTIONr_scbond_it0.97315002
X-RAY DIFFRACTIONr_scangle_it1.6194.512781
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A5974medium positional0.390.5
12B5974medium positional0.420.5
13C5974medium positional0.450.5
14D5974medium positional0.430.5
15E5974medium positional0.370.5
16F5974medium positional0.390.5
21A6391medium positional0.440.5
22B6391medium positional0.510.5
23C6391medium positional0.510.5
24D6391medium positional0.460.5
25E6391medium positional0.460.5
26F6391medium positional0.470.5
11A5974medium thermal0.332
12B5974medium thermal0.32
13C5974medium thermal0.282
14D5974medium thermal0.282
15E5974medium thermal0.282
16F5974medium thermal0.292
21A6391medium thermal0.352
22B6391medium thermal0.32
23C6391medium thermal0.282
24D6391medium thermal0.282
25E6391medium thermal0.292
26F6391medium thermal0.282
LS refinement shellResolution: 2.73→2.801 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 732 -
Rwork0.366 14499 -
obs--99.77 %
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)
10.8673-0.28810.81150.6177-0.63882.07240.00620.2652-0.0019-0.0628-0.0275-0.10540.1850.03860.0212-0.36940.01660.0934-0.3582-0.0065-0.285727.641792.100753.6886
21.3645-0.69840.79840.4863-0.78571.57070.2463-0.0806-0.0491-0.1732-0.04780.00850.03090.2359-0.1986-0.0535-0.00940.0088-0.398-0.0843-0.098359.440957.123199.3916
31.7860.31851.25290.59130.5811.7232-0.115-0.3364-0.0636-0.20540.0851-0.0038-0.34760.17850.0299-0.2672-0.1790.1378-0.0672-0.0185-0.2751101.0083169.84074.5214
40.8143-0.13180.53790.6588-0.05751.38170.27430.1713-0.1745-0.34440.02540.29160.34580.124-0.29970.0793-0.0524-0.2055-0.2934-0.0158-0.029170.5681134.2451-41.1594
51.17890.24251.06780.19540.55781.86050.26440.2379-0.19160.1778-0.01940.02620.6282-0.0662-0.24490.0768-0.1492-0.033-0.1701-0.0006-0.082147.324133.68818.4933
61.27450.05450.9970.40690.34323.3785-0.1524-0.07630.03720.00680.134-0.0111-0.03330.53170.0184-0.3723-0.03230.0897-0.24350.0126-0.281481.7247169.743363.8724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 9019 - 901
2X-RAY DIFFRACTION2BB9 - 9019 - 901
3X-RAY DIFFRACTION3CC9 - 9019 - 901
4X-RAY DIFFRACTION4DD7 - 9017 - 901
5X-RAY DIFFRACTION5EE16 - 90116 - 901
6X-RAY DIFFRACTION6FF20 - 90120 - 901

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