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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 / homologyPolyketide synthase, thioesterase domain / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase, N-terminal domain / ACP-like superfamily / Polyketide synthase, docking domain superfmaily / NAD(P)-binding domain superfamily / Ketoacyl-synthetase, C-terminal extension / Alpha/Beta hydrolase fold ...Polyketide synthase, thioesterase domain / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase, N-terminal domain / ACP-like superfamily / Polyketide synthase, docking domain superfmaily / NAD(P)-binding domain superfamily / Ketoacyl-synthetase, C-terminal extension / Alpha/Beta hydrolase fold / Polyketide synthase, beta-ketoacyl synthase domain / Polyketide synthase, phosphopantetheine-binding domain / KR domain / Polyketide synthase, acyl transferase domain / Beta-ketoacyl synthase, active site / Thiolase-like / Acyl transferase/acyl hydrolase/lysophospholipase / Beta-ketoacyl synthase, C-terminal domain / Polyketide synthase, docking domain / Acyl transferase / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal / Polyketide synthase, ketoreductase domain / Phosphopantetheine binding ACP domain / Phosphopantetheine attachment site / Acyl transferase domain superfamily / Thioesterase / Erythronolide synthase docking / Ketoacyl-synthetase C-terminal extension / Phosphopantetheine attachment site. / Beta-ketoacyl synthases active site. / Carrier protein (CP) domain profile. / Thioesterase domain / 6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / phosphopantetheine binding / biosynthetic process / hydrolase activity, acting on ester bonds / transferase activity / 6-deoxyerythronolide-B synthase EryA3, modules 5 and 6 / EryAIII
Function and homology information
Specimen sourceSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 2.73 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 26, 2006 / Release: Jul 11, 2006
RevisionDateData content typeGroupProviderType
1.0Jul 11, 2006Structure modelrepositoryInitial release
1.1Apr 29, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelAdvisory / 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
Polyers587,8866
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
Polyers195,9622
Non-polymers3465
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)6440
ΔGint (kcal/M)-65
Surface area (Å2)64740
MethodPISA,PQS
2
C: 6-Deoxyerythronolide B Synthase
D: 6-Deoxyerythronolide B Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,2477
Polyers195,9622
Non-polymers2855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)6490
ΔGint (kcal/M)-64
Surface area (Å2)65000
MethodPISA,PQS
3
E: 6-Deoxyerythronolide B Synthase
F: 6-Deoxyerythronolide B Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,3438
Polyers195,9622
Non-polymers3816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)6190
ΔGint (kcal/M)-71
Surface area (Å2)63730
MethodPISA,PQS
Unit cell
γ
α
β
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-MC 1 2 1
DetailsDimer. Molecules A and B, C and D, E and F form biological dimers.

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Components

#1: Protein/peptide
6-Deoxyerythronolide B Synthase / DEBS


Mass: 97980.922 Da / Num. of mol.: 6
Fragment: ketosynthase-acyltransferase didomain of didomain module 5
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Genus: Saccharopolyspora / Gene: eryA / Plasmid name: pAYC10 / Genus (production host): Escherichia / 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 / Formula: C2H3O2 / Acetate
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 35.453 Da / Num. of mol.: 5 / Formula: Cl / Chloride
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Formula: H2O / Water

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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 / Density percent sol: 63.55 %
Crystal growTemp: 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 kelvins
SourceSource: SYNCHROTRON / Type: SSRL BEAMLINE BL11-1 / Synchrotron site: SSRL / Beamline: BL11-1 / Wavelength: 0.9392, 0.9793, 0.9789
DetectorType: ADSC QUANTUM 315 / Details: mirrors / Detector: CCD / Collection date: May 13, 2005
RadiationMonochromator: Single Crystal Si(111) / Diffraction protocol: MAD / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
10.93921.0
20.97931.0
30.97891.0
ReflectionB iso Wilson estimate: 57.3 Å2 / D resolution high: 2.73 Å / D resolution low: 48.17 Å / Number all: 206652 / Number obs: 206652 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.112 / NetI over sigmaI: 8.3 / Redundancy: 3.8 % / Percent possible obs: 99.8
Reflection shellRmerge I obs: 0.68 / Highest resolution: 2.73 Å / Lowest resolution: 2.88 Å / MeanI over sigI obs: 1.9 / Number unique all: 30114 / Redundancy: 3.8 % / Percent possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
SHELXphasing
RESOLVEphasing
RefineMethod to determine structure: MAD / Correlation coeff Fo to Fc: 0.94 / Correlation coeff Fo to Fc free: 0.914 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 34.897 / Overall SU ML: 0.299 / R Free selection details: RANDOM / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.607 / Overall ESU R Free: 0.318
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 66.11 Å2 / Aniso B11: -0.18 Å2 / Aniso B12: 0 Å2 / Aniso B13: -4.51 Å2 / Aniso B22: 0.62 Å2 / Aniso B23: 0 Å2 / Aniso B33: -3.53 Å2
Least-squares processR factor R free: 0.255 / R factor R work: 0.21612 / R factor all: 0.2181 / R factor obs: 0.2181 / Highest resolution: 2.73 Å / Lowest resolution: 48.03 Å / Number reflection R free: 10395 / Number reflection all: 206602 / Number reflection obs: 196207 / Percent reflection R free: 5 / Percent reflection obs: 99.75
Refine hist #LASTHighest resolution: 2.73 Å / Lowest resolution: 48.03 Å
Number of atoms included #LASTProtein: 39038 / Nucleic acid: 0 / Ligand: 54 / Solvent: 310 / Total: 39402
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02239848
X-RAY DIFFRACTIONr_bond_other_d0.0010.02036915
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.95754195
X-RAY DIFFRACTIONr_angle_other_deg0.8293.00084883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1475.0005263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49522.3771742
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.57515.0005903
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.08815.000455
X-RAY DIFFRACTIONr_chiral_restr0.0780.2006034
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02046032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0208461
X-RAY DIFFRACTIONr_nbd_refined0.2320.2009308
X-RAY DIFFRACTIONr_nbd_other0.1820.20038594
X-RAY DIFFRACTIONr_nbtor_refined0.1850.20019624
X-RAY DIFFRACTIONr_nbtor_other0.0890.20025861
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.200932
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0760.2006
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.20050
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.200205
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.2009
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6061.50030548
X-RAY DIFFRACTIONr_mcbond_other0.0931.50010844
X-RAY DIFFRACTIONr_mcangle_it0.7722.00041414
X-RAY DIFFRACTIONr_scbond_it0.9703.00015002
X-RAY DIFFRACTIONr_scangle_it1.6194.50012781
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

Dom IDAuth asym IDEns IDNumberTypeRms dev positionWeight position
1A15974medium positional0.390.50
2B15974medium positional0.420.50
3C15974medium positional0.450.50
4D15974medium positional0.430.50
5E15974medium positional0.370.50
6F15974medium positional0.390.50
1A26391medium positional0.440.50
2B26391medium positional0.510.50
3C26391medium positional0.510.50
4D26391medium positional0.460.50
5E26391medium positional0.460.50
6F26391medium positional0.470.50
1A15974medium thermal0.332.00
2B15974medium thermal0.302.00
3C15974medium thermal0.282.00
4D15974medium thermal0.282.00
5E15974medium thermal0.282.00
6F15974medium thermal0.292.00
1A26391medium thermal0.352.00
2B26391medium thermal0.302.00
3C26391medium thermal0.282.00
4D26391medium thermal0.282.00
5E26391medium thermal0.292.00
6F26391medium thermal0.282.00
Refine LS shellHighest resolution: 2.73 Å / R factor R free: 0.368 / R factor R work: 0.366 / Lowest resolution: 2.801 Å / Number reflection R free: 732 / Number reflection R work: 14499 / Total number of bins used: 20 / Percent reflection obs: 99.77
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.8673-0.28810.81150.6177-0.63882.07240.00620.2652-0.0019-0.0628-0.0275-0.10540.18500.03860.0212-0.36940.01660.0934-0.3582-0.0065-0.285727.641792.100753.6886
21.3645-0.69840.79840.4863-0.78571.57070.2463-0.0806-0.0491-0.1732-0.04780.00850.03090.2359-0.1986-0.0535-0.00940.0088-0.3980-0.0843-0.098359.440957.123199.3916
31.78600.31851.25290.59130.58101.7232-0.1150-0.3364-0.0636-0.20540.0851-0.0038-0.34760.17850.0299-0.2672-0.17900.1378-0.0672-0.0185-0.2751101.0083169.84074.5214
40.8143-0.13180.53790.6588-0.05751.38170.27430.1713-0.1745-0.34440.02540.29160.34580.1240-0.29970.0793-0.0524-0.2055-0.2934-0.0158-0.029170.5681134.2451-41.1594
51.17890.24251.06780.19540.55781.86050.26440.2379-0.19160.1778-0.01940.02620.6282-0.0662-0.24490.0768-0.1492-0.0330-0.1701-0.0006-0.082147.3240133.688018.4933
61.27450.05450.99700.40690.34323.3785-0.1524-0.07630.03720.00680.1340-0.0111-0.03330.53170.0184-0.3723-0.03230.0897-0.24350.0126-0.281481.7247169.743363.8724
Refine TLS group

End auth seq ID: 901 / End label seq ID: 901 / Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDBeg label asym IDBeg label seq IDEnd auth asym IDEnd label asym IDRefine TLS ID
1A9A9AA1
2B9B9BB2
3C9C9CC3
4D7D7DD4
5E16E16EE5
6F20F20FF6

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