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Yorodumi- PDB-7e1r: Crystal structure of Dehydrogenase/isomerase FabX from Helicobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7e1r | ||||||
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Title | Crystal structure of Dehydrogenase/isomerase FabX from Helicobacter pylori in complex with holo-ACP | ||||||
Components |
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Keywords | FLAVOPROTEIN / Unsaturated fatty acid biosynthesis / FMN / 4Fe-4S cluster | ||||||
Function / homology | Function and homology information Kdo2-lipid A biosynthetic process / nitronate monooxygenase activity / dioxygenase activity / phosphopantetheine binding / acyl carrier activity / 4 iron, 4 sulfur cluster binding / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.795 Å | ||||||
Authors | Zhou, J.S. / Zhang, L. / Zhang, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Helicobacter pylori FabX contains a [4Fe-4S] cluster essential for unsaturated fatty acid synthesis. Authors: Zhou, J. / Zhang, L. / Zeng, L. / Yu, L. / Duan, Y. / Shen, S. / Hu, J. / Zhang, P. / Song, W. / Ruan, X. / Jiang, J. / Zhang, Y. / Zhou, L. / Jia, J. / Hang, X. / Tian, C. / Lin, H. / Chen, ...Authors: Zhou, J. / Zhang, L. / Zeng, L. / Yu, L. / Duan, Y. / Shen, S. / Hu, J. / Zhang, P. / Song, W. / Ruan, X. / Jiang, J. / Zhang, Y. / Zhou, L. / Jia, J. / Hang, X. / Tian, C. / Lin, H. / Chen, H.Z. / Cronan, J.E. / Bi, H. / Zhang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e1r.cif.gz | 186.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e1r.ent.gz | 144.9 KB | Display | PDB format |
PDBx/mmJSON format | 7e1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e1r_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7e1r_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7e1r_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 7e1r_validation.cif.gz | 49.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/7e1r ftp://data.pdbj.org/pub/pdb/validation_reports/e1/7e1r | HTTPS FTP |
-Related structure data
Related structure data | 7e1qC 7e1sC 4iqlS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 40871.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) Gene: AM497_02530, B0X24_07955, B0X43_08370, BB415_05730, BB461_06560, BV499_05860, BZK23_04525, C2840_03950, C2844_03945, C2S07_02490, DB320_04065, DD749_04060, DD750_03440, DD754_03975, DD776_ ...Gene: AM497_02530, B0X24_07955, B0X43_08370, BB415_05730, BB461_06560, BV499_05860, BZK23_04525, C2840_03950, C2844_03945, C2S07_02490, DB320_04065, DD749_04060, DD750_03440, DD754_03975, DD776_04195, DD780_03830, EC524_01920, EC526_01900, EC558_05290, ECB91_05230, ECC12_03705, ECC36_03060, EGW00_07215, HPY1846_07480 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B2E3F3 #2: Protein | Mass: 9363.529 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The fusion protein of 2 ACP (residues 1-35 and 36-78) Source: (gene. exp.) Helicobacter pylori (bacteria) Gene: acpP, AOD76_0203840, ECC46_04805, acpP, ACM27_07645, AEY52_04040, B0X51_03260, B0X63_05470, BB389_02970, BB399_05955, BB436_06630, BFR58_08310, BGL65_04100, BGL68_01550, C2R80_01075, C2S26_ ...Gene: acpP, AOD76_0203840, ECC46_04805, acpP, ACM27_07645, AEY52_04040, B0X51_03260, B0X63_05470, BB389_02970, BB399_05955, BB436_06630, BFR58_08310, BGL65_04100, BGL68_01550, C2R80_01075, C2S26_06440, D2C76_07900, DB320_02975, DD746_02765, DD771_02980, EC538_03680, EC543_05790, EC570_04560, EC596_03965, EC600_01035, ECC09_04825, ECC20_05115, ECC36_06460, HPF20_0453, HPF211_0816, HPF63_0811, HPF94_0692, HPK25_01094, HPMKF3_0586, HPMKM1_0566, HPMKM6_0558, HPY1198_07760, NCTC12823_00687 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0T6M3S8, UniProt: A0A0B2DUK3 |
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-Non-polymers , 4 types, 50 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.16 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES pH 7.0, 20% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.795→99.576 Å / Num. obs: 21529 / % possible obs: 97.2 % / Redundancy: 6.6 % / CC1/2: 0.987 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 2310 / CC1/2: 0.847 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IQL Resolution: 2.795→48.736 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.65 Å2 / Biso mean: 49.8445 Å2 / Biso min: 9.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.795→48.736 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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