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- PDB-1i8o: RHODOPSEUDOMONAS PALUSTRIS CYT C2 AMMONIA COMPLEX AT 1.15 ANGSTRO... -

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Basic information

Entry
Database: PDB / ID: 1i8o
TitleRHODOPSEUDOMONAS PALUSTRIS CYT C2 AMMONIA COMPLEX AT 1.15 ANGSTROM RESOLUTION
ComponentsCYTOCHROME C2
KeywordsELECTRON TRANSPORT / CYTOCHROME / HEME / AMMONIA / OXIDIZED
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 / AMMONIA / Cytochrome c2
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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: Crystal Structure of Oxidized and Reduced Cytochrome from Rhodopseudomonas Palustris: Relationship Between Hydrogen-Bonding Network of the Conservative Water Molecule and Reduction Potential
Authors: Geremia, S. / Calligaris, M. / Garau, G. / Vaccari, L. / Viezzoli, M.S. / Randaccio, L.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Crystallization and X-Ray Structure Determination O Cytochrome C2 Fromrhodobacter Sphaeroides in Three Crystal Forms
Authors: Axelrod, H. / Feher, G. / Allen, J.P. / Chirino, A.J. / Day, M.W. / Hsu, B.T. / Rees, D.C.
#4: 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.
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: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 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 / pdbx_struct_special_symmetry / 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_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
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0155
Polymers12,1871
Non-polymers8284
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: CYTOCHROME C2
hetero molecules

A: CYTOCHROME C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,02910
Polymers24,3742
Non-polymers1,6558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area4280 Å2
ΔGint-101 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.950, 64.950, 68.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

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Components

#1: Protein CYTOCHROME C2


Mass: 12186.983 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-NH3 / AMMONIA


Mass: 17.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 3.2 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 60% AMMONIUM SULPHATE, 0.1 M TRIS PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
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 / 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: 1.15→15.2 Å / Num. all: 59295 / Num. obs: 55707 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 7.1
Reflection shellResolution: 1.15→1.21 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 5.9 / % possible all: 99.1
Reflection
*PLUS
Num. obs: 57362 / % possible obs: 99.3 % / Num. measured all: 364867
Reflection shell
*PLUS
% possible obs: 96.7 % / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
AMoREphasing
SHELXVERSION 97-1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HH7

1hh7


Resolution: 1.15→15.2 Å / Num. parameters: 10378 / Num. restraintsaints: 11837 / Cross valid method: FREE R / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1616 2972 5 %RANDOM
Rwork0.1345 ---
all0.1402 58679 --
obs0.1401 55707 99.1 %-
Refine analyzeNum. disordered residues: 1
Refinement stepCycle: LAST / Resolution: 1.15→15.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms855 0 54 239 1148
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d2.1
Software
*PLUS
Name: SHELX / Version: VERSION 97-1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.139 / Rfactor Rfree: 0.167 / Rfactor Rwork: 0.151
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.6

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