+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16893 | |||||||||
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Title | Low resolution map of RhiE with flexible ACP linker | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Polyketide / TRANSFERASE | |||||||||
Biological species | Mycetohabitans rhizoxinica (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.42 Å | |||||||||
Authors | Capper MJ / Koehnke J | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: To Be Published Title: Structural Analysis of a Chain-Branching Polyketide Synthase Module Authors: Dell M / Tran MA / Capper MJ / Sundaram S / Fiedler J / Koehnke J / Hellmich U / Hertwick C | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16893.map.gz | 4.1 MB | EMDB map data format | |
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Header (meta data) | emd-16893-v30.xml emd-16893.xml | 15.6 KB 15.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16893_fsc.xml | 4.2 KB | Display | FSC data file |
Images | emd_16893.png | 111.7 KB | ||
Masks | emd_16893_msk_1.map | 8 MB | Mask map | |
Filedesc metadata | emd-16893.cif.gz | 5.7 KB | ||
Others | emd_16893_half_map_1.map.gz emd_16893_half_map_2.map.gz | 7.4 MB 7.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16893 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16893 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16893.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 2.03 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16893_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16893_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16893_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Homodimeric complex of RhiE KSB domains
Entire | Name: Homodimeric complex of RhiE KSB domains |
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Components |
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-Supramolecule #1: Homodimeric complex of RhiE KSB domains
Supramolecule | Name: Homodimeric complex of RhiE KSB domains / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycetohabitans rhizoxinica (bacteria) |
Molecular weight | Theoretical: 230 KDa |
-Macromolecule #1: RhiE KSBACP
Macromolecule | Name: RhiE KSBACP / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycetohabitans rhizoxinica (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MKHHHHHHHH GGLVPRGSHG GSSGERVEDN ELANYIAVIG LGGYYPGADS IDELWQNLAN GVDCMSDFPA DRWDHSKIYY KNRKVLGKT TCINGSFIKD VDKFDYSYFK MPKVYADHMS PEVRLFLQVA VHTFEDAGYS KETLLSRYNG DVGVLLGTMS N DYHYYGFE ...String: MKHHHHHHHH GGLVPRGSHG GSSGERVEDN ELANYIAVIG LGGYYPGADS IDELWQNLAN GVDCMSDFPA DRWDHSKIYY KNRKVLGKT TCINGSFIKD VDKFDYSYFK MPKVYADHMS PEVRLFLQVA VHTFEDAGYS KETLLSRYNG DVGVLLGTMS N DYHYYGFE SNVFRGSMAS GSGMATIPMT VSYFYGLTGP SLFIDTMCSS SSTCIHTACQ MLKHDETKMV LAGGLNLMYH PY TTVNTSQ GNFTSITSES VNSYGVGADG TVIGEGIGAV LLKRLDRAIA DRDQIYGVIK GSAMTNAGER NGFNVPNPDL QTL AIRQAM DQAKVHPSSI SYIEGHGSGT KLGDPIEVLG LNNAFRWATD DKQFCYLGSI KSNIGHLLAA SGIAGLTKTL LQFK HKQIA PSIHSSQLNQ DIDFADTPFV VPQQLIEWRQ PERIINGRKQ VFPRRAGLTS IAAGGMNAHM IVEEYPEPAD SAGQI SEDQ LVFVFSVHKL ALLAQNLTSF RDWLASSEAP LAQIAYTLQV GKNNLRNRLA IRCRTRQALS RALNACIDGH YQSSAD SKI FYRFQESDAV QPLESDLNDP LAPLLTQWLN GDSQVDWASL YAQPPVRISL PAYRFEKTRC WYTEEGYESS IVNPLMF KN KLHPLVAKNC STPQPGAIFR TDFVEDELLD YVYSGRGGRR LSAFNFADVA LAMPALASRF DGRTLSVSCA FEHYIADW T TVTGLEYRLF EIDSEQLELE FDFRRSGEQP THLGFAVINP LTSDEPPLPQ QWLDDARELL NRQALQAGRQ LSAAEVSQR LAQAGYDFAP YLDHDGELTI GRSGLVLKGR PPVNRHNHYA DNVQLSPYLA TTIDKALYLL LDELGLPQGR VIVRNIERLC CYHTPAGGF SVVLSGIGLN DNELSLSLLV LDEREQICVK LDKVSLYLGK QEVASVDRKH SLLTGEERMA EFKQEAKPQA D DSEAGFGE KILAFIQQEL QDKLGFAADI GESTQVHDLG LDSIMVVQLT DSVNKRFGTK LMPDLFYEKQ QLGELVARLE AA A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL |
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Buffer | pH: 8 / Component - Concentration: 20.0 mM / Component - Name: Tris-HClTris / Details: 20 mM Tris-HCl pH 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK III |
Details | Monodisperse sample in minimal buffer |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 120000 |
Sample stage | Specimen holder model: JEOL / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3579 / Average electron dose: 53.9 e/Å2 |