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- PDB-6zmq: Cytochrome c Heme Lyase CcmF -

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Basic information

Entry
Database: PDB / ID: 6zmq
TitleCytochrome c Heme Lyase CcmF
ComponentsCytochrome C-type biogenesis protein ccmF
KeywordsMEMBRANE PROTEIN / Heme lyase cytochrome c maturation membrane protein cytochrome
Function / homology
Function and homology information


heme transmembrane transporter activity / cytochrome complex assembly / heme binding / metal ion binding / membrane
Similarity search - Function
Cytochrome c-type biogenesis protein / Cytochrome c-type biogenesis protein CcmF, C-terminal / Cytochrome c-type biogenesis protein CcmF C-terminal / Cytochrome c assembly protein / Cytochrome C assembly protein
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATIDYLETHANOLAMINE / Cytochrome C-type biogenesis protein ccmF
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.67 Å
AuthorsBrausemann, A. / Einsle, O.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC 1381, project ID 403222702 Germany
European Research Council (ERC)310656 Germany
CitationJournal: 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
DepositionJul 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome C-type biogenesis protein ccmF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2748
Polymers72,7001
Non-polymers4,5747
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-61 kcal/mol
Surface area28180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.720, 128.270, 134.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome C-type biogenesis protein ccmF


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
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.03 Å3/Da / Density % sol: 75.53 % / Description: plates
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 19, 2017
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.67→3.06 Å / Redundancy: 23.5 % / Num. unique obs: 779 / CC1/2: 0.502 / % possible all: 58.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.3085 1487 5.11 %RANDOM
Rwork0.2707 27588 --
obs0.2726 15576 44.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.67 Å2 / Biso mean: 61.3781 Å2 / Biso min: 19.09 Å2
Refinement stepCycle: final / Resolution: 2.67→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4636 0 313 17 4966
Biso mean--65.55 34.33 -
Num. residues----589
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.67-2.750.403280.48811261342
2.75-2.850.1993140.36752382524
2.85-2.960.5845140.43324044187
2.96-3.10.3375700.3924943101317
3.1-3.260.451750.37051648172329
3.26-3.470.43831360.35962156229238
3.47-3.730.33351470.31542807295449
3.73-4.110.29652160.28373702391866
4.11-4.70.29572500.22914583483381
4.7-5.920.31062830.26815379566295
5.92-48.150.28342740.25955602587698
Refinement TLS params.Method: refined / Origin x: -40.7078 Å / Origin y: 4.3014 Å / Origin z: 142.115 Å
111213212223313233
T0.3155 Å2-0.0591 Å2-0.0029 Å2-0.1331 Å20.0474 Å2--0.2863 Å2
L1.1731 °2-0.0495 °2-0.1158 °2-0.2384 °20.4493 °2--0.8942 °2
S0.0478 Å °0.0479 Å °-0.0156 Å °-0.1193 Å °0.0296 Å °-0.0122 Å °-0.0649 Å °0.0757 Å °-0 Å °
Refinement TLS groupSelection details: all

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