+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27534 | |||||||||
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Title | CYP102A1 in Open Conformation | |||||||||
Map data | ||||||||||
Sample |
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Keywords | cytochrome P450 electron transfer protein dynamic CYP102A1 / OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Priestia megaterium NBRC 15308 = ATCC 14581 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||
Authors | Su M / Xu H | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Insight into the conformational dynamics of cytochrome P450 CYP102A1 enzyme using Cryo-EM Authors: Su M / Xu H | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27534.map.gz | 21 MB | EMDB map data format | |
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Header (meta data) | emd-27534-v30.xml emd-27534.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
Images | emd_27534.png | 108.9 KB | ||
Others | emd_27534_half_map_1.map.gz emd_27534_half_map_2.map.gz | 20.6 MB 20.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27534 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27534 | HTTPS FTP |
-Related structure data
Related structure data | 8dmeMC 8dmgC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27534.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 2.02 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_27534_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27534_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CYP102A1
Entire | Name: CYP102A1 |
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Components |
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-Supramolecule #1: CYP102A1
Supramolecule | Name: CYP102A1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: BM3 CYP102A |
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Source (natural) | Organism: Priestia megaterium NBRC 15308 = ATCC 14581 (bacteria) |
Molecular weight | Theoretical: 240 KDa |
-Macromolecule #1: Bifunctional cytochrome P450/NADPH--P450 reductase
Macromolecule | Name: Bifunctional cytochrome P450/NADPH--P450 reductase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: unspecific monooxygenase |
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Source (natural) | Organism: Priestia megaterium NBRC 15308 = ATCC 14581 (bacteria) Strain: ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19 |
Molecular weight | Theoretical: 116.541734 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: KEMPQPKTFG ELKNLPLLNT DKPVQALMKI ADELGEIFKF EAPGRVTRYL SSQRLIKEAC DESRFDKNLS QALKFVRDFF GDGLFTSWT HEKNWKKAHN ILLPSFSQQA MKGYHAMMVD IAVQLVQKWE RLNADEHIEV PEDMTRLTLD TIGLCGFNYR F NSFYRDQP ...String: KEMPQPKTFG ELKNLPLLNT DKPVQALMKI ADELGEIFKF EAPGRVTRYL SSQRLIKEAC DESRFDKNLS QALKFVRDFF GDGLFTSWT HEKNWKKAHN ILLPSFSQQA MKGYHAMMVD IAVQLVQKWE RLNADEHIEV PEDMTRLTLD TIGLCGFNYR F NSFYRDQP HPFITSMVRA LDEAMNKLQR ANPDDPAYDE NKRQFQEDIK VMNDLVDKII ADRKASGEQS DDLLTHMLNG KD PETGEPL DDENIRYQII TFLIAGHETT SGLLSFALYF LVKNPHVLQK AAEEAARVLV DPVPSYKQVK QLKYVGMVLN EAL RLWPTA PAFSLYAKED TVLGGEYPLE KGDELMVLIP QLHRDKTIWG DDVEEFRPER FENPSAIPQH AFKPFGNGQR ACIG QQFAL HEATLVLGMM LKHFDFEDHT NYELDIKETL TLKPEGFVVK AKSKKIPLKK VRKKAENAHN TPLLVLYGSN MGTAE GTAR DLADIAMSKG FAPQVATLDS HAGNLPREGA VLIVTASYNG HPPDNAKQFV DWLDQASADE VKGVRYSVFG CGDKNW ATT YQKVPAFIDE TLAAKGAENI ADRGEADASD DFEGTYEEWR EHMWSDVAAY FNLDIENSED NKSTLSLQFV DSAADMP LA KMHGAFSTNV VASKELQQPG SARSTRHLEI ELPKEASYQE GDHLGVIPRN YEGIVNRVTA RFGLDASQQI RLEAEEEK L AHLPLAKTVS VEELLQYVEL QDPVTRTQLR AMAAKTVCPP HKVELEALLE KQAYKEQVLA KRLTMLELLE KYPACEMKF SEFIALLPSI RPRYYSISSS PRVDEKQASI TVSVVSGEAW SGYGEYKGIA SNYLAELQEG DTITCFISTP QSEFTLPKDP ETPLIMVGP GTGVAPFRGF VQARKQLKEQ GQSLGEAHLY FGCRSPHEDY LYQEELENAQ SEGIITLHTA FSRMPNQPKT Y VQHVMEQD GKKLIELLDQ GAHFYICGDG SQMAPAVEAT LMKSYADVHQ VSEADARLWL QQLEEKGRYA KDVWAG UniProtKB: Bifunctional cytochrome P450/NADPH--P450 reductase |
-Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE
Macromolecule | Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 2 / Formula: HEM |
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Molecular weight | Theoretical: 616.487 Da |
Chemical component information | ChemComp-HEM: |
-Macromolecule #3: 6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl...
Macromolecule | Name: 6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-benzimidazole type: ligand / ID: 3 / Number of copies: 2 / Formula: 1C6 |
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Molecular weight | Theoretical: 329.417 Da |
Chemical component information | ChemComp-1C6: |
-Macromolecule #4: FLAVIN MONONUCLEOTIDE
Macromolecule | Name: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 2 / Formula: FMN |
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Molecular weight | Theoretical: 456.344 Da |
Chemical component information | ChemComp-FMN: |
-Macromolecule #5: FLAVIN-ADENINE DINUCLEOTIDE
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 2 / Formula: FAD |
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Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ChemComp-FAD: |
-Macromolecule #6: SULFATE ION
Macromolecule | Name: SULFATE ION / type: ligand / ID: 6 / Number of copies: 6 / Formula: SO4 |
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Molecular weight | Theoretical: 96.063 Da |
Chemical component information | ChemComp-SO4: |
-Macromolecule #7: TETRAETHYLENE GLYCOL
Macromolecule | Name: TETRAETHYLENE GLYCOL / type: ligand / ID: 7 / Number of copies: 4 / Formula: PG4 |
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Molecular weight | Theoretical: 194.226 Da |
Chemical component information | ChemComp-PG4: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.4 / Component - Concentration: 50.0 mM / Component - Formula: K2HPO4-KH2PO4-KCL / Component - Name: sodium phosphate + potassium chloride Details: Fresh prepare sodium phosphate (50mM) + potassium chloride (150mM), pH7.4 and filter with 0.22um filters. |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
Details | The CYP102A1 sample purify and concentrated to 5mg/ml. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 15.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 204254 |