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- PDB-2fwt: Crystal structure of DHC purified from Rhodobacter sphaeroides -

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Basic information

Entry
Database: PDB / ID: 2fwt
TitleCrystal structure of DHC purified from Rhodobacter sphaeroides
ComponentsDHC, diheme cytochrome c
KeywordsELECTRON TRANSPORT / cytochrome c / diheme protein / electron transfer / sphaeroides heme protein / oxygen-binding
Function / homologyDihaem cytochrome c / Dihaem cytochrome c / Multiheme cytochrome superfamily / metal ion binding / HEME C / DHC, diheme cytochrome c
Function and homology information
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsLeys, D.
CitationJournal: Biochemistry / Year: 2006
Title: Structural and Functional Studies on DHC, the Diheme Cytochrome c from Rhodobacter sphaeroides, and Its Interaction with SHP, the sphaeroides Heme Protein
Authors: Gibson, H.R. / Mowat, C.G. / Miles, C.S. / Li, B.R. / Leys, D. / Reid, G.A. / Chapman, S.K.
History
DepositionFeb 3, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 2, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DHC, diheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7543
Polymers13,5171
Non-polymers1,2372
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.790, 72.790, 51.484
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein DHC, diheme cytochrome c


Mass: 13517.294 Da / Num. of mol.: 1 / Fragment: residues 12-136 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: Q3J4W3
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG 3000, 0.2M ammonium acetate, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9, 1.74
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2001
RadiationMonochromator: diamond / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
21.741
ReflectionResolution: 1.85→30 Å / Num. all: 13408 / Num. obs: 13408 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.4
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 2.8 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.339 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.152 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19272 659 4.9 %RANDOM
Rwork0.14987 ---
all0.1519 12739 --
obs0.1519 12739 100 %-
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: 19.946 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.38 Å20 Å2
2--0.77 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms823 0 86 115 1024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022945
X-RAY DIFFRACTIONr_bond_other_d0.0010.02808
X-RAY DIFFRACTIONr_angle_refined_deg1.5942.2371308
X-RAY DIFFRACTIONr_angle_other_deg0.95831863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1075110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24523.43832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52815125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.026155
X-RAY DIFFRACTIONr_chiral_restr0.120.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021035
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02164
X-RAY DIFFRACTIONr_nbd_refined0.3190.2218
X-RAY DIFFRACTIONr_nbd_other0.1870.2778
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2438
X-RAY DIFFRACTIONr_nbtor_other0.0920.2450
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0650.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3180.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5551.5703
X-RAY DIFFRACTIONr_mcbond_other0.4371.5225
X-RAY DIFFRACTIONr_mcangle_it1.9982886
X-RAY DIFFRACTIONr_scbond_it2.563479
X-RAY DIFFRACTIONr_scangle_it3.3444.5418
X-RAY DIFFRACTIONr_rigid_bond_restr1.76632111
X-RAY DIFFRACTIONr_sphericity_free6.4753115
X-RAY DIFFRACTIONr_sphericity_bonded1.77631717
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 48 -
Rwork0.147 897 -
obs--100 %

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