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- PDB-2dge: Crystal structure of oxidized cytochrome C6A from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 2dge
TitleCrystal structure of oxidized cytochrome C6A from Arabidopsis thaliana
ComponentsCytochrome c6
KeywordsELECTRON TRANSPORT / Cytochrome c6A / electron transfer / heme exposure / Arabidopsis thaliana
Function / homology
Function and homology information


chloroplast thylakoid lumen / photosynthesis / chloroplast / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c6 / Cytochrome C oxidase, cbb3-type, subunit III / 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 c6, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChida, H. / Yokoyama, T. / Kawai, F. / Nakazawa, A. / Akazaki, H. / Takayama, Y. / Hirano, T. / Suruga, K. / Satoh, T. / Yamada, S. ...Chida, H. / Yokoyama, T. / Kawai, F. / Nakazawa, A. / Akazaki, H. / Takayama, Y. / Hirano, T. / Suruga, K. / Satoh, T. / Yamada, S. / Kawachi, R. / Unzai, S. / Nishio, T. / Park, S.-Y. / Oku, T.
CitationJournal: Febs Lett. / Year: 2006
Title: Crystal structure of oxidized cytochrome c(6A) from Arabidopsis thaliana
Authors: Chida, H. / Yokoyama, T. / Kawai, F. / Nakazawa, A. / Akazaki, H. / Takayama, Y. / Hirano, T. / Suruga, K. / Satoh, T. / Yamada, S. / Kawachi, R. / Unzai, S. / Nishio, T. / Park, S.-Y. / Oku, T.
History
DepositionMar 11, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 2.0Dec 24, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _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_modification_feature.auth_comp_id / _pdbx_modification_feature.label_comp_id / _pdbx_modification_feature.ref_comp_id / _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.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 3.0Aug 12, 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_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c6
B: Cytochrome c6
C: Cytochrome c6
D: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,47710
Polymers46,8644
Non-polymers2,6136
Water4,468248
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cytochrome c6
C: Cytochrome c6
hetero molecules

B: Cytochrome c6
D: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,47710
Polymers46,8644
Non-polymers2,6136
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area8140 Å2
ΔGint-187 kcal/mol
Surface area20690 Å2
MethodPISA
3
A: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4023
Polymers11,7161
Non-polymers6862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
B: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4023
Polymers11,7161
Non-polymers6862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
C: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3372
Polymers11,7161
Non-polymers6211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
D: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3372
Polymers11,7161
Non-polymers6211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.443, 51.843, 53.685
Angle α, β, γ (deg.)82.51, 62.08, 63.26
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cytochrome c6 / Cytochrome c6 like protein / Soluble cytochrome f / Cytochrome c553 / Cytochrome c-553 / Cytochrome ...Cytochrome c6 like protein / Soluble cytochrome f / Cytochrome c553 / Cytochrome c-553 / Cytochrome c-552 / Atc6


Mass: 11716.122 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ATC6 / Plasmid: pSTV28ccm-A-H / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q93VA3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-HEC / HEME C


Mass: 620.519 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H36FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.5 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEGMME550, MES, ZnSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2004 / Details: Si(III)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 59952 / Num. obs: 59952 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.9
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.183 / % possible all: 66.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GDV

1gdv


Resolution: 1.5→31.47 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.573 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.083 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21451 3029 5.1 %RANDOM
Rwork0.18624 ---
all0.18767 56923 --
obs0.18767 56923 100 %-
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: 20.187 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20.27 Å20.37 Å2
2--0.62 Å2-0.22 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3186 0 174 248 3608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223495
X-RAY DIFFRACTIONr_angle_refined_deg1.1222.1064716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8535402
X-RAY DIFFRACTIONr_chiral_restr0.0750.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022712
X-RAY DIFFRACTIONr_nbd_refined0.1930.21563
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2205
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.216
X-RAY DIFFRACTIONr_mcbond_it0.7061.51994
X-RAY DIFFRACTIONr_mcangle_it1.38523199
X-RAY DIFFRACTIONr_scbond_it1.98931484
X-RAY DIFFRACTIONr_scangle_it3.3054.51517
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.255 138
Rwork0.23 3018

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