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- PDB-3a9f: Crystal structure of the C-terminal domain of cytochrome cz from ... -

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Basic information

Entry
Database: PDB / ID: 3a9f
TitleCrystal structure of the C-terminal domain of cytochrome cz from Chlorobium tepidum
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / alpha helix / cytochrome / mono heme
Function / homology
Function and homology information


photosynthesis / electron transfer activity / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Photosystem P840 reaction-centre, cytochrome c-551 / Photosystem P840 reaction-centre cytochrome c-551 / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / TRIETHYLENE GLYCOL / Cytochrome c
Similarity search - Component
Biological speciesChlorobaculum tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsHirano, Y. / Higuchi, M. / Azai, C. / Oh-oka, H. / Miki, K. / Wang, Z.-Y.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of the electron carrier domain of the reaction center cytochrome c(z) subunit from green photosynthetic bacterium Chlorobium tepidum
Authors: Hirano, Y. / Higuchi, M. / Azai, C. / Oh-Oka, H. / Miki, K. / Wang, Z.-Y.
History
DepositionOct 25, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3109
Polymers20,2832
Non-polymers2,0277
Water4,846269
1
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3566
Polymers10,1421
Non-polymers1,2145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9543
Polymers10,1421
Non-polymers8132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.619, 74.619, 111.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome c / cytochrome cz / Photosystem P840 reaction center cytochrome c-551


Mass: 10141.683 Da / Num. of mol.: 2 / Fragment: C-terminal domain, UNP residues 117-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Gene: pscC / Plasmid: pET-20b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: O07091

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Non-polymers , 7 types, 276 molecules

#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 3.82 Å3/Da / Density % sol: 67.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.4M ammonium sulfate, 2% PEG 400, 0.1M sodium citrate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 1, 2007
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 73534 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 71.5
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 4.4 / % possible all: 94.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
OASISmodel building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
OASISphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→37.32 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.032 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.15454 3660 5 %RANDOM
Rwork0.13809 ---
obs0.13891 69589 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2--0.61 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.3→37.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 137 269 1611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221423
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3512.1771936
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8785163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23223.63655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.80115232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.551158
X-RAY DIFFRACTIONr_chiral_restr0.0750.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211061
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3611.5786
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.25921273
X-RAY DIFFRACTIONr_scbond_it2.883637
X-RAY DIFFRACTIONr_scangle_it4.2034.5658
X-RAY DIFFRACTIONr_rigid_bond_restr1.27631423
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 223 -
Rwork0.202 5009 -
obs--95.08 %

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