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- PDB-8gth: Crystal strucuture of cyt c551 from anoxygenic phototrophic bacte... -

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Basic information

Entry
Database: PDB / ID: 8gth
TitleCrystal strucuture of cyt c551 from anoxygenic phototrophic bacterium Roseiflexus castenholzii
ComponentsCytochrome c class I
KeywordsELECTRON TRANSPORT / electron transfer protein
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
HEME C / Cytochrome c class I
Similarity search - Component
Biological speciesRoseiflexus castenholzii DSM 13941 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMin, Z.Z. / Meng, H.L. / Xu, X.L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171227 China
National Natural Science Foundation of China (NSFC)31870740 China
National Natural Science Foundation of China (NSFC)31570738 China
CitationJournal: Plant Commun. / Year: 2024
Title: A cytochrome c 551 mediates the cyclic electron transport chain of the anoxygenic phototrophic bacterium Roseiflexus castenholzii.
Authors: Yu, L. / Min, Z. / Liu, M. / Xin, Y. / Liu, A. / Kuang, J. / Wu, W. / Wu, J. / He, H. / Xin, J. / Blankenship, R.E. / Tian, C. / Xu, X.
History
DepositionSep 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c class I
B: Cytochrome c class I
C: Cytochrome c class I
E: Cytochrome c class I
F: Cytochrome c class I
D: Cytochrome c class I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,32312
Polymers73,6126
Non-polymers3,7116
Water00
1
A: Cytochrome c class I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8872
Polymers12,2691
Non-polymers6191
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c class I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8872
Polymers12,2691
Non-polymers6191
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome c class I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8872
Polymers12,2691
Non-polymers6191
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Cytochrome c class I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8872
Polymers12,2691
Non-polymers6191
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
F: Cytochrome c class I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8872
Polymers12,2691
Non-polymers6191
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
D: Cytochrome c class I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8872
Polymers12,2691
Non-polymers6191
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.630, 71.630, 349.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein
Cytochrome c class I


Mass: 12268.652 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseiflexus castenholzii DSM 13941 (bacteria)
Strain: DSM 13941 / HLO8 / Gene: Rcas_2631 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7NME2
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
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: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 1.5 M Lithium sulfate monohydrate 0.1 M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97991 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97991 Å / Relative weight: 1
ReflectionResolution: 3.1→31.43 Å / Num. obs: 17547 / % possible obs: 99.78 % / Redundancy: 22.9 % / Biso Wilson estimate: 74.97 Å2 / CC1/2: 0.994 / Net I/σ(I): 8.1
Reflection shellResolution: 3.1→3.211 Å / Num. unique obs: 1693 / CC1/2: 0.569

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Cootmodel building
Cootmodel building
xia2data reduction
xia2data scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→31.43 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / Phase error: 26.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2717 887 5.06 %
Rwork0.2417 --
obs-17542 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→31.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4563 0 258 0 4821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024964
X-RAY DIFFRACTIONf_angle_d0.6046824
X-RAY DIFFRACTIONf_dihedral_angle_d13.3451772
X-RAY DIFFRACTIONf_chiral_restr0.036661
X-RAY DIFFRACTIONf_plane_restr0.003906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.290.35331470.3222689X-RAY DIFFRACTION100
3.29-3.550.3641170.29682729X-RAY DIFFRACTION100
3.55-3.90.31941540.26672721X-RAY DIFFRACTION100
3.9-4.470.25541550.23492753X-RAY DIFFRACTION100
4.47-5.620.24011560.22012785X-RAY DIFFRACTION100
5.63-31.430.23181580.20812979X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -0.0389 Å / Origin y: 32.446 Å / Origin z: 30.2843 Å
111213212223313233
T0.4177 Å20.0359 Å2-0.0862 Å2-0.365 Å20.0006 Å2--0.5377 Å2
L0.6775 °20.2085 °20.3096 °2-0.7473 °2-0.7077 °2--2.3953 °2
S0.0018 Å °0.0102 Å °0.101 Å °-0.0108 Å °0.0258 Å °0.0519 Å °-0.1136 Å °-0.0853 Å °-0.0235 Å °
Refinement TLS groupSelection details: all

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