+Open data
-Basic information
Entry | Database: PDB / ID: 6zmq | |||||||||
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Title | Cytochrome c Heme Lyase CcmF | |||||||||
Components | Cytochrome C-type biogenesis protein ccmF | |||||||||
Keywords | MEMBRANE PROTEIN / Heme lyase cytochrome c maturation membrane protein cytochrome | |||||||||
Function / homology | Function and homology information heme transmembrane transporter activity / cytochrome complex assembly / membrane => GO:0016020 / heme binding Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.67 Å | |||||||||
Authors | Brausemann, A. / Einsle, O. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Nat.Chem.Biol. / Year: 2021 Title: Architecture of the membrane-bound cytochrome c heme lyase CcmF. Authors: Brausemann, A. / Zhang, L. / Ilcu, L. / Einsle, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zmq.cif.gz | 267.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zmq.ent.gz | 213 KB | Display | PDB format |
PDBx/mmJSON format | 6zmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/6zmq ftp://data.pdbj.org/pub/pdb/validation_reports/zm/6zmq | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 72699.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: ccmF, TT_C1038 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72IU4 | ||||||
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#2: Chemical | ChemComp-HEM / | ||||||
#3: Sugar | #4: Chemical | ChemComp-PTY / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.03 Å3/Da / Density % sol: 75.53 % / Description: plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 18-19 % (v/v) low molecular weight polyethylene glycols (PEG 400, PEG 550 MME, PEG 600, PEG 1000), 0.1 M BisTris pH 6.5, 150 mM MgCl2, 4 % (v/v) trifluorethanol PH range: 6.2-6.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 19, 2017 |
Radiation | Monochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→92.98 Å / Num. obs: 15589 / % possible obs: 91.4 % / Redundancy: 26.8 % / CC1/2: 1 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.67→3.06 Å / Redundancy: 23.5 % / Num. unique obs: 779 / CC1/2: 0.502 / % possible all: 58.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.67→48.15 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 41.74 / 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: 149.67 Å2 / Biso mean: 61.3781 Å2 / Biso min: 19.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.67→48.15 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Origin x: -40.7078 Å / Origin y: 4.3014 Å / Origin z: 142.115 Å
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Refinement TLS group | Selection details: all |