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Basic information

Entry
Database: PDB / ID: 5awi
TitleDomain-swapped cytochrome cb562 dimer
ComponentsSoluble cytochrome b562
KeywordsELECTRON TRANSPORT
Function / homologyCytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / electron transfer activity / periplasmic space / iron ion binding / heme binding / HEME C / Soluble cytochrome b562
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMiyamoto, T. / Kuribayashi, M. / Nagao, S. / Shomura, Y. / Higuchi, Y. / Hirota, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS26288080 Japan
JSPS15K13744 Japan
CitationJournal: Chem Sci / Year: 2015
Title: Domain-swapped cytochrome cb562 dimer and its nanocage encapsulating a Zn-SO4 cluster in the internal cavity
Authors: Miyamoto, T. / Kuribayashi, M. / Nagao, S. / Shomura, Y. / Higuchi, Y. / Hirota, S.
History
DepositionJul 3, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 2.0Oct 2, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_source / entity / entity_src_gen / pdbx_database_related / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
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 / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_related.content_type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Nov 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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.ptnr1_symmetry / _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.ptnr2_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble cytochrome b562
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,35314
Polymers23,3702
Non-polymers1,98312
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-108 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.608, 94.608, 94.608
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-204-

SO4

21B-204-

SO4

31A-304-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 1 - 106 / Label seq-ID: 1 - 106

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Soluble cytochrome b562 / Cytochrome b-562


Mass: 11685.159 Da / Num. of mol.: 2 / Fragment: UNP residues 23-128 / Mutation: R98C, Y101C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / Strain (production host): JCB387 / References: UniProt: P0ABE7
#2: Chemical ChemComp-HEC / HEME C / Heme C


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


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG MME 350, 6 mM ZnSO4, 750 mM MES buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.501
11L, -K, H20.499
ReflectionResolution: 1.85→20 Å / Num. obs: 24682 / % possible obs: 100 % / Redundancy: 16.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 69
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 6.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BC5

2bc5


Resolution: 1.85→19.31 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.701 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20487 1199 4.9 %RANDOM
Rwork0.17997 ---
obs0.18125 23154 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: 36.971 Å2
Baniso -1Baniso -2Baniso -3
1--5.62 Å220.61 Å2-7.05 Å2
2--21.13 Å2-12.38 Å2
3----15.5 Å2
Refinement stepCycle: 1 / Resolution: 1.85→19.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 108 61 1799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021785
X-RAY DIFFRACTIONr_bond_other_d0.0030.021676
X-RAY DIFFRACTIONr_angle_refined_deg1.1762.0522396
X-RAY DIFFRACTIONr_angle_other_deg0.9283.0023858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5795210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.62627.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58515320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.727156
X-RAY DIFFRACTIONr_chiral_restr0.0950.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022004
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02346
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_it0.8232.031846
X-RAY DIFFRACTIONr_mcbond_other0.822.03845
X-RAY DIFFRACTIONr_mcangle_it1.3633.0421054
X-RAY DIFFRACTIONr_mcangle_other1.3643.0421055
X-RAY DIFFRACTIONr_scbond_it1.0932.038929
X-RAY DIFFRACTIONr_scbond_other0.8892.031907
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4092.9881324
X-RAY DIFFRACTIONr_long_range_B_refined3.32315.5042058
X-RAY DIFFRACTIONr_long_range_B_other3.31915.4042045
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5482 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 77 -
Rwork0.268 1697 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0697-0.12820.07380.72370.09041.6632-0.0205-0.1666-0.01120.19840.0646-0.08750.0583-0.0122-0.04410.15330.02210.00770.08690.01430.1416-7.49625.05927.194
21.3125-0.94920.06051.2277-0.16262.06460.21460.43570.1526-0.243-0.2934-0.126-0.02730.08270.07880.10440.04140.03940.22320.06940.1796-1.5630.607-4.276
30.04510.02120.02630.0233-0.00320.04270.00130.0792-0.0593-0.02150.021-0.02480.03190.0564-0.02230.0941-0.014-0.02020.1935-0.10710.1154-9.97133.54813.559
42.204-1.71024.00012.1429-3.36077.3409-0.0778-0.0672-0.00630.15110.1080.0731-0.1674-0.1447-0.03020.0788-0.03020.0490.2037-0.070.0854-11.85332.2357.888
53.87530.5257-0.2652.0283.20235.3796-0.0573-0.0561-0.03750.1391-0.03470.05360.2277-0.02940.0920.2124-0.0556-0.01710.08080.03810.0811-1.1933.6599.198
60.0598-0.0849-0.18190.38610.60591.01090.0275-0.0363-0.09090.0022-0.0218-0.099-0.0031-0.0026-0.00570.1156-0.0248-0.00990.08850.11540.3512-9.63236.79217.882
70.4101-0.5596-0.86320.7861.18381.81870.00530.00530.0244-0.07890.03230.056-0.04630.0026-0.03770.2405-0.1092-0.18280.14910.1880.4057-5.05133.78713.722
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 52
2X-RAY DIFFRACTION1B53 - 106
3X-RAY DIFFRACTION1B201
4X-RAY DIFFRACTION2B1 - 52
5X-RAY DIFFRACTION2A53 - 106
6X-RAY DIFFRACTION2A201
7X-RAY DIFFRACTION3A202
8X-RAY DIFFRACTION4B202
9X-RAY DIFFRACTION5B203
10X-RAY DIFFRACTION6A203
11X-RAY DIFFRACTION7A204

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