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- PDB-2bh5: X-ray structure of the M100K variant of ferric cyt c-550 from Par... -

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Basic information

Entry
Database: PDB / ID: 2bh5
TitleX-ray structure of the M100K variant of ferric cyt c-550 from Paracoccus versutus determined at 295 K.
ComponentsCYTOCHROME C-550
KeywordsELECTRON TRANSFER / C-TYPE CYTOCHROME / HEME / AXIAL LIGAND / 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: 1.95 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 7, 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 1.3Dec 13, 2023Group: 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.0Sep 2, 2026Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_contact_author / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_validate_chiral / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _pdbx_contact_author.country / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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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
Polymers14,1551
Non-polymers6211
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.457, 43.011, 87.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME C-550


Mass: 14154.857 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PARACOCCUS VERSUTUS (bacteria) / Plasmid: PUC19_M100K/PEC86 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MV1190 / References: UniProt: Q00499
#2: Chemical ChemComp-HEC / HEME C


Mass: 620.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H36FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN X MET 100 TO LYS
Has protein modificationY
Sequence detailsWILD-TYPE GENE ACCESSION CODE

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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 Å3/Da / Density % sol: 38.7 %
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 3, 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: 1.95→43.85 Å / Num. obs: 9207 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.6
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.8 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1COT

1cot


Resolution: 1.95→43.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1 AND 122-134 ARE NOT OBSERVED
RfactorNum. reflection% reflectionSelection details
Rfree0.233 434 4.7 %RANDOM
Rwork0.185 ---
obs0.187 8711 99.3 %-
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: 33.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å20 Å2
2--1.52 Å20 Å2
3----2.78 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 0 43 32 989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022991
X-RAY DIFFRACTIONr_bond_other_d0.0010.02870
X-RAY DIFFRACTIONr_angle_refined_deg1.1532.1041351
X-RAY DIFFRACTIONr_angle_other_deg0.66332049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.075120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5726.66739
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01215170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.249151
X-RAY DIFFRACTIONr_chiral_restr0.0660.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021091
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02164
X-RAY DIFFRACTIONr_nbd_refined0.2770.3215
X-RAY DIFFRACTIONr_nbd_other0.1830.3798
X-RAY DIFFRACTIONr_nbtor_refined0.1850.5478
X-RAY DIFFRACTIONr_nbtor_other0.0910.5480
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.569
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.34
X-RAY DIFFRACTIONr_symmetry_vdw_other0.0830.315
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.54
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.143780
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4914959
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8353479
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5584390
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: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.368 28
Rwork0.222 591

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