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- PDB-3vrd: Crystal structure of flavocytochrome c from Thermochromatium tepidum -

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Basic information

Entry
Database: PDB / ID: 3vrd
TitleCrystal structure of flavocytochrome c from Thermochromatium tepidum
Components(Flavocytochrome c ...) x 2
KeywordsELECTRON TRANSPORT/OXIDOREDUCTASE / sulfide oxidation / Heme c binding / FAD binding / ELECTRON TRANSPORT-OXIDOREDUCTASE complex
Function / homology
Function and homology information


flavin adenine dinucleotide binding / periplasmic space / electron transfer activity / oxidoreductase activity / iron ion binding / heme binding
Similarity search - Function
Flavocytochrome C Sulfide Dehydrogenase; Chain A Domain 3 / Flavocytochrome c sulphide dehydrogenase, flavin-binding domain / Flavocytochrome c sulphide dehydrogenase, flavin-binding / Flavocytochrome c sulphide dehydrogenase, flavin-binding domain superfamily / Flavocytochrome c sulphide dehydrogenase, flavin-binding / Cytochrome c4-like / Cytochrome C oxidase, cbb3-type, subunit III / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / FAD/NAD-linked reductase, dimerisation domain superfamily / Cytochrome c-like domain ...Flavocytochrome C Sulfide Dehydrogenase; Chain A Domain 3 / Flavocytochrome c sulphide dehydrogenase, flavin-binding domain / Flavocytochrome c sulphide dehydrogenase, flavin-binding / Flavocytochrome c sulphide dehydrogenase, flavin-binding domain superfamily / Flavocytochrome c sulphide dehydrogenase, flavin-binding / Cytochrome c4-like / Cytochrome C oxidase, cbb3-type, subunit III / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / FAD/NAD-linked reductase, dimerisation domain superfamily / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / HEME C / NITRATE ION / Flavocytochrome c heme subunit / Flavocytochrome c flavin subunit
Similarity search - Component
Biological speciesThermochromatium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHirano, Y. / Kimura, Y. / Suzuki, H. / Miki, K. / Wang, Z.-Y.
CitationJournal: Biochemistry / Year: 2012
Title: Structure Analysis and Comparative Characterization of the Cytochrome c' and Flavocytochrome c from Thermophilic Purple Photosynthetic Bacterium Thermochromatium tepidum
Authors: Hirano, Y. / Kimura, Y. / Suzuki, H. / Miki, K. / Wang, Z.-Y.
History
DepositionApr 9, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Derived calculations / Refinement description
Category: pdbx_distant_solvent_atoms / pdbx_validate_close_contact ...pdbx_distant_solvent_atoms / pdbx_validate_close_contact / software / struct_conn / struct_conn_type
Item: _software.name / _struct_conn_type.id
Revision 1.2Nov 8, 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 / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavocytochrome c heme subunit
B: Flavocytochrome c flavin subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,80710
Polymers62,3842
Non-polymers2,4238
Water9,962553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-73 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.617, 140.617, 57.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Flavocytochrome c ... , 2 types, 2 molecules AB

#1: Protein Flavocytochrome c heme subunit / fcca subunit


Mass: 19484.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D0G7Q3
#2: Protein Flavocytochrome c flavin subunit / fccb subunit


Mass: 42900.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D0G7Q4

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Non-polymers , 5 types, 561 molecules

#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 18% PEG 3000, 0.2M potassium nitrate, 0.05M MES-NaOH, pH 6.0, 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 210 / Detector: CCD / Date: Dec 1, 2007 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 84166 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 22.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 3 / % possible all: 84.5

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FCD

1fcd


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.228 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19511 4208 5 %RANDOM
Rwork0.15969 ---
all0.16148 84163 --
obs0.16148 79955 93.34 %-
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: 13.292 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4379 0 165 553 5097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.024672
X-RAY DIFFRACTIONr_angle_refined_deg2.7442.0086371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5845574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66824.607191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30315728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9741520
X-RAY DIFFRACTIONr_chiral_restr0.1980.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.0213585
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 260 -
Rwork0.223 5146 -
obs--83.58 %

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