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- PDB-1e29: PSII associated cytochrome C549 from Synechocystis sp. -

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Basic information

Entry
Database: PDB / ID: 1.0E+29
TitlePSII associated cytochrome C549 from Synechocystis sp.
ComponentsCYTOCHROME C549
KeywordsELECTRON TRANSPORT / PSII ASSOCIATED CYTOCHROME / CYTOCHROME / LOW POTENTIAL / BIS_HISTIDINYL / PSII MODULATOR
Function / homology
Function and homology information


plasma membrane-derived thylakoid photosystem II / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / respiratory electron transport chain / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / 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
HEME C / Photosystem II extrinsic protein V
Similarity search - Component
Biological speciesSYNECHOCYSTIS SP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.21 Å
AuthorsFrazao, C. / Enguita, F.J. / Coelho, R. / Sheldrick, G.M.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2001
Title: Crystal Structure of Low-Potential Cytochrome C549 from Synechocystis Sp. Pcc 6803 at 1.21A Resolution
Authors: Frazao, C. / Enguita, F.J. / Coelho, R. / Sheldrick, G.M. / Navarro, J.A. / Hervas, M. / De La Rosa, M.A. / Carrondo, M.A.
History
DepositionMay 19, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _struct_conn_type.id
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.6Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C549
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8735
Polymers15,1351
Non-polymers7394
Water4,017223
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)34.220, 86.860, 97.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

21A-354-

HOH

31A-479-

HOH

41A-481-

HOH

51A-523-

HOH

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Components

#1: Protein CYTOCHROME C549


Mass: 15134.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SYNECHOCYSTIS SP (bacteria) / Strain: PCC 6803 / References: UniProt: Q55013
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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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: 1.99 Å3/Da / Density % sol: 48.7 %
Description: LOCALIZATION OF FE ATOM BY PATTERSON ANALYSIS OF SUPER- SHARPENED NATIVE OR ANOMALOUS DIFFERENCE MAPS, FOLLOWED BY FE- ANCHORED ROTATION SEARCH OF CYS-GLY-GLY-CYS-HIS+HEME FRAGMENT AND ...Description: LOCALIZATION OF FE ATOM BY PATTERSON ANALYSIS OF SUPER- SHARPENED NATIVE OR ANOMALOUS DIFFERENCE MAPS, FOLLOWED BY FE- ANCHORED ROTATION SEARCH OF CYS-GLY-GLY-CYS-HIS+HEME FRAGMENT AND EXPANSION OF THIS SEED FRAGMENT TO FINAL SOLUTION
Crystal growMethod: vapor diffusion, sitting drop / pH: 8.5
Details: SITTING DROP, VAPOUR DIFFUSION, 16% PEG 8000, O.2 M CALCIUM ACETATE, 0.1 M TRIS/HCL, PH = 8.5
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 %PEG80001drop
20.2 Mcalcium acetate1drop
30.1 MTris-HCl1drop
430 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8374
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1998
RadiationMonochromator: GE SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8374 Å / Relative weight: 1
ReflectionResolution: 1.21→97.7 Å / Num. obs: 42933 / % possible obs: 95.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 31.1
Reflection shellResolution: 1.21→1.23 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.8 / % possible all: 85.9
Reflection
*PLUS
Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 85.9 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 1.21→97.7 Å / Num. parameters: 12079 / Num. restraintsaints: 14469 / Cross valid method: FREE R-VALUE / σ(F): 0
StereochEM target val spec case: HEME TARGET VALUES FROM CYTOCHROME C6, STRUCTURE 3(1995)1159-1169
Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 2158 5 %RANDOM
all0.1528 42953 --
obs0.1486 -94.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 1051 / Occupancy sum non hydrogen: 1329.93
Refinement stepCycle: LAST / Resolution: 1.21→97.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 46 223 1334
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0.018
X-RAY DIFFRACTIONs_from_restr_planes0.0283
X-RAY DIFFRACTIONs_zero_chiral_vol0.077
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.078
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.043
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.06
X-RAY DIFFRACTIONs_approx_iso_adps0.115
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.1486
Solvent computation
*PLUS
Displacement parameters
*PLUS

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