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- PDB-2bgv: X-ray structure of ferric cytochrome c-550 from Paracoccus versutus -

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Basic information

Entry
Database: PDB / ID: 2bgv
TitleX-ray structure of ferric cytochrome c-550 from Paracoccus versutus
ComponentsCYTOCHROME C-550
KeywordsELECTRON TRANSFER / C-TYPE CYTOCHROME / HEME GROUP / PYRROLIDONE CARBOXYLIC ACID
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / 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 c-550
Similarity search - Component
Biological speciesPARACOCCUS VERSUTUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWorrall, J.A.R. / Van Roon, A.-M.M. / Ubbink, M. / Canters, G.W.
CitationJournal: FEBS J. / Year: 2005
Title: The Effect of Replacing the Axial Methionine Ligand with a Lysine Residue in Cytochrome C-550 from Paracoccus Versutus Assessed by X-Ray Crystallography and Unfolding.
Authors: Worrall, J.A.R. / Van Roon, A.-M.M. / Ubbink, M. / Canters, G.W.
History
DepositionJan 5, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: CYTOCHROME C-550
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7752
Polymers14,1571
Non-polymers6191
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.102, 57.102, 66.616
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 C-550


Mass: 14156.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HEME, PROTOPORPHYRIN IX / Source: (gene. exp.) PARACOCCUS VERSUTUS (bacteria) / Plasmid: PEG400.TV1 / Production host: PARACOCCUS DENITRIFICANS (bacteria) / Strain (production host): 2131 / References: UniProt: Q00499
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPTM: BINDS 1 HEME GROUP PER SUBUNIT
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: 1.8 Å3/Da / Density % sol: 32.9 %
Crystal growpH: 9 / Details: 3.2 M AMMONIUM SULFATE, 0.1 M BICINE PH 9

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR78 / Wavelength: 1.54
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 2003 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→45 Å / Num. obs: 9898 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 14.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 20.5
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.24 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE OF M100K CYTOCHROME C-550

Resolution: 1.9→43.44 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.191 436 4.8 %RANDOM
Rwork0.158 ---
obs0.16 8690 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms900 0 43 50 993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022991
X-RAY DIFFRACTIONr_bond_other_d0.0010.02871
X-RAY DIFFRACTIONr_angle_refined_deg1.1582.1061348
X-RAY DIFFRACTIONr_angle_other_deg0.72132059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8695118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.95226.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9815178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.972151
X-RAY DIFFRACTIONr_chiral_restr0.0870.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021081
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02162
X-RAY DIFFRACTIONr_nbd_refined0.2870.3221
X-RAY DIFFRACTIONr_nbd_other0.1880.3795
X-RAY DIFFRACTIONr_nbtor_refined0.1790.5486
X-RAY DIFFRACTIONr_nbtor_other0.090.5488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.572
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.312
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.331
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3910.515
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1122.5773
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3493948
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6512500
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5493398
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.207 28
Rwork0.144 624

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