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- PDB-1ls9: Structure of the Cytochrome c6 from the Green Alga Cladophora glo... -

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Basic information

Entry
Database: PDB / ID: 1ls9
TitleStructure of the Cytochrome c6 from the Green Alga Cladophora glomerata
ComponentsCYTOCHROME C6
KeywordsELECTRON TRANSPORT / omega loop / antiparallel beta-sheet / PROTOPORPHYRIN IX CONTAINING FE / heme / haem / CYTOCHROME
Function / homology
Function and homology information


chloroplast thylakoid lumen / photosynthesis / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c6 / Cytochrome c, class IC / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c6
Similarity search - Component
Biological speciesCladophora glomerata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsCarpentier, W.
CitationJournal: Biochemistry / Year: 2002
Title: Structural Basis for the Molecular Properties of Cytochrome C(6)
Authors: Dikiy, A. / Carpentier, W. / Vandenberghe, I. / Borsari, M. / Safarov, N. / Dikaya, E. / Van Beeumen, J. / Ciurli, S.
History
DepositionMay 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4602
Polymers9,8441
Non-polymers6161
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.063, 46.063, 100.526
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CYTOCHROME C6


Mass: 9843.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cladophora glomerata (plant) / References: UniProt: P83391
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.2 M Na-acetate, 0.1 M Na-cacodylate, pH 6.5, 30% w/v PEG 8000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
220 mMTris-HCl1droppH7.6
30.2 Msodium acetate1reservoir
40.1 Msodium cacodylate1reservoirpH6.5
530 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8015 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 17, 2001 / Details: 165-mm MAR CCD
RadiationMonochromator: Triangular, Bent mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8015 Å / Relative weight: 1
ReflectionResolution: 1.3→14.8906 Å / Num. obs: 27067 / % possible obs: 98.4 % / Redundancy: 20.25 % / Rsym value: 0.053 / Net I/σ(I): 25.3
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 38.68 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.311 / % possible all: 97.6
Reflection
*PLUS
Lowest resolution: 14891 Å / Num. measured all: 114176 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 97.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CTJ

1ctj


Resolution: 1.3→14.684 Å / SU B: 0.55284 / SU ML: 0.02413 / Cross valid method: THROUGHOUT / ESU R: 0.0435 / ESU R Free: 0.04757 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19034 1358 5 %RANDOM
Rwork0.14339 ---
all0.157 ---
obs0.14922 25709 98.6 %-
Displacement parametersBiso mean: 16.595 Å2
Baniso -1Baniso -2Baniso -3
1-0.4835 Å20 Å20 Å2
2--0.4835 Å20 Å2
3---0.0177 Å2
Refinement stepCycle: LAST / Resolution: 1.3→14.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms674 0 43 200 917
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0240.02
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.0590.05
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.1380.15
X-RAY DIFFRACTIONp_singtor_nbd0.1650.3
X-RAY DIFFRACTIONp_multtor_nbd0.2780.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.0710.3
X-RAY DIFFRACTIONp_xhyhbond_nbd00.3
X-RAY DIFFRACTIONp_special_tor015
X-RAY DIFFRACTIONp_planar_tor5.37
X-RAY DIFFRACTIONp_staggered_tor11.215
X-RAY DIFFRACTIONp_transverse_tor17.820
X-RAY DIFFRACTIONp_mcbond_it2.4052
X-RAY DIFFRACTIONp_mcangle_it2.83
X-RAY DIFFRACTIONp_scbond_it3.3842
X-RAY DIFFRACTIONp_scangle_it4.293
LS refinement shellResolution: 1.3→1.32 Å
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.19 / Rfactor Rwork: 0.143
Solvent computation
*PLUS
Displacement parameters
*PLUS

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