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- PDB-1i8p: STRUCTURE DETERMINATION OF THE FERROCYTOCHROME C2 FROM RHODOPSEUD... -

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Basic information

Entry
Database: PDB / ID: 1i8p
TitleSTRUCTURE DETERMINATION OF THE FERROCYTOCHROME C2 FROM RHODOPSEUDOMONAS PALUSTRIS
ComponentsCYTOCHROME C2
KeywordsELECTRON TRANSPORT / ELECTRON CARRIER / HEME PROTEIN / CYTOCHROME / C2 / REDUCED / RHODOPSEUDOMONAS PALUSTRIS
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: 1.95 Å
AuthorsGarau, G. / Geremia, 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: Acta Crystallogr.,Sect.D / Year: 2000
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: To be Published
Title: CLEAVAGE OF THE IRON-METHIONINE BOND IN CYTOCHROME C-TYPE PROTEIN: X-RAY STRUCTURE OF THE RHODOPSEUDOMONAS PALUSTRIS CYTOCHROME C2 AMMONIA COMPLEX AT 1.15 A RESOLUTION
Authors: Geremia, S. / Garau, G. / Sgarra, R. / Viezzoli, M.S. / Randaccio, L.
History
DepositionMar 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
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 2.1Aug 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
Remark 999SEQUENCE PCA 1: GLN 1 HAS BEEN CYCLIZED TO PYRROLIDONE CARBOXYLIC ACID. THIS PROTEIN WAS EXPRESSED ...SEQUENCE PCA 1: GLN 1 HAS BEEN CYCLIZED TO PYRROLIDONE CARBOXYLIC ACID. THIS PROTEIN WAS EXPRESSED FROM A DIFFERENT STRAIN THAN THE DATABASE PROTEIN SWISSPROT ENTRY P00091 AND HAS SEVERAL MUTATIONS: G29A, I64V, N65P, N68A, AND D80E.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)51,2228
Polymers48,7484
Non-polymers2,4744
Water11,043613
1
A: 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
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
3
C: 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
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
Unit cell
Length a, b, c (Å)50.119, 71.706, 67.357
Angle α, β, γ (deg.)90.00, 93.67, 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-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 42% AMMONIUM SULPHATE,0.1 M SODIUM CITRATE PH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 8, 2000 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.95→20 Å / Num. all: 106868 / Num. obs: 34702 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.175 / Net I/σ(I): 6.4
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 106868
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FJ0

1fj0


Resolution: 1.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1742 5 %RANDOM
Rwork0.1605 ---
all0.1919 106868 --
obs0.1942 32939 99.7 %-
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---1 Å20 Å2
3---1 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3420 0 172 613 4205
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0290.022
X-RAY DIFFRACTIONp_mcbond_it2.6791.5
X-RAY DIFFRACTIONp_mcangle_it3.6982
X-RAY DIFFRACTIONp_scbond_it5.9093
X-RAY DIFFRACTIONp_scangle_it8.9324.5

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