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- PDB-1fj0: STRUCTURE DETERMINATION OF THE FERRICYTOCHROME C2 FROM RHODOPSEUD... -

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Basic information

Entry
Database: PDB / ID: 1fj0
TitleSTRUCTURE DETERMINATION OF THE FERRICYTOCHROME C2 FROM RHODOPSEUDOMONAS PALUSTRIS
ComponentsCYTOCHROME C2
KeywordsELECTRON TRANSPORT / ELECTRON CARRIER / HEME PROTEIN
Function / homology
Function and homology information


photosynthesis / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / 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 / Cytochrome c2
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGeremia, S.
Citation
Journal: Protein Sci. / Year: 2002
Title: Cleavage of the iron-methionine bond in c-type cytochromes: Crystal structure of oxidized and reduced cytochrome c(2) from Rhodopseudomonas palustris and its ammonia complex.
Authors: Geremia, S. / Garau, G. / Vaccari, L. / Sgarra, R. / Viezzoli, M.S. / Calligaris, M. / Randaccio, L.
#1: Journal: To be Published
Title: Crystallization and Preliminary X-Ray Analysis of Two pH-Dependent Forms of Cytochrome C2 from Rhodopseudomonas Palustris
Authors: Garau, G. / Geremia, S. / Randaccio, L. / Vaccari, L. / Viezzoli, M.S.
#2: Journal: Nature / Year: 1979
Title: Cytochrome C2 Sequence Variation Among the Recognised Species of Purple Nonsulphur Photosynthetic Bacteria
Authors: Ambler, R.P. / Daniel, M. / Hermoso, J. / Meyer, T.E. / Bartsch, R.G. / Kamen, M.D.
#3: Journal: J.Mol.Biol. / Year: 1995
Title: Refined Crystal Structure of Ferrocytochrome C2 From Rhodopseudomonas Viridis at 1.6 A Resolution
Authors: Sogabe, S. / Miki, K.
History
DepositionAug 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jan 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id
Revision 3.1Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 3.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C2
B: CYTOCHROME C2
C: CYTOCHROME C2
D: CYTOCHROME C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,50611
Polymers48,7484
Non-polymers2,7587
Water11,764653
1
A: CYTOCHROME C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9023
Polymers12,1871
Non-polymers7152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTOCHROME C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8052
Polymers12,1871
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CYTOCHROME C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9944
Polymers12,1871
Non-polymers8073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CYTOCHROME C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8052
Polymers12,1871
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.310, 71.530, 66.660
Angle α, β, γ (deg.)90.00, 93.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CYTOCHROME C2


Mass: 12186.983 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / Strain: 42 OL / References: UniProt: P00091
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / 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: 2.46 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: ammonium sulfate, ferricyanide, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19.0 mg/mlprotein1droppH6.0
220 mMphosphate1drop
342-44 %satammonium sulfate1reservoir
40.1 Mcitrate1reservoirpH4.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 23, 1999 / Details: mirrors
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 194662 / Num. obs: 51959 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 13.42 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.6 / Num. unique all: 7539 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 194662
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2c2c

2c2c


Resolution: 1.7→50 Å / SU B: 2.19354 / SU ML: 0.07236 / σ(F): 0 / σ(I): 0 / ESU R: 0.11194 / ESU R Free: 0.11096 / Stereochemistry target values: Engh & Huber
Details: The following NCS restraints were released: main-chain and side-chain of THR94, PHE95 and side-chain of LYS11, ASP20, LYS21, GLU53, LYS76, LYS96, LYS 114. The NCS restraints are as follows: ...Details: The following NCS restraints were released: main-chain and side-chain of THR94, PHE95 and side-chain of LYS11, ASP20, LYS21, GLU53, LYS76, LYS96, LYS 114. The NCS restraints are as follows: Delta 1- RMS:0.076, Sigma:0.500, Delta 2- RMS:0.101, Sigma 0.500, Delta 3- RMS:0.056, Sigma:0.500, Delta 4- RMS:0.045, Sigma:0.500.
RfactorNum. reflection% reflectionSelection details
Rfree0.21793 2648 5 %RANDOM
Rwork0.17775 ---
all-51970 --
obs-49259 99.9 %-
Displacement parametersBiso mean: 16.44 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3420 0 188 653 4261
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0250.04
X-RAY DIFFRACTIONp_planar_d0.030.05
X-RAY DIFFRACTIONp_plane_restr0.021
X-RAY DIFFRACTIONp_chiral_restr0.1130.15
X-RAY DIFFRACTIONp_mcbond_it2.7150.5
X-RAY DIFFRACTIONp_mcangle_it3.7813
X-RAY DIFFRACTIONp_scbond_it6.2452
X-RAY DIFFRACTIONp_scangle_it7.0763
X-RAY DIFFRACTIONp_singtor_nbd0.1670.3
X-RAY DIFFRACTIONp_multtor_nbd0.2580.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1080.3
X-RAY DIFFRACTIONp_planar_tor3.57
X-RAY DIFFRACTIONp_staggered_tor15.215
X-RAY DIFFRACTIONp_transverse_tor13.520
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_bond_d / Dev ideal: 0.01

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