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- PDB-5z25: Trimeric Alpha-Helix-Inserted Circular Permutant of Cytochrome c555 -

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Basic information

Entry
Database: PDB / ID: 5z25
TitleTrimeric Alpha-Helix-Inserted Circular Permutant of Cytochrome c555
ComponentsCytochrome c552
KeywordsELECTRON TRANSPORT / Permutant
Function / homology
Function and homology information


electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c, class ID / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / Cytochrome c552
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOda, A. / Nagao, S. / Yamanaka, M. / Ueda, I. / Shibata, N. / Higuchi, Y. / Hirota, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPS26288080 Japan
JSPS15K13744 Japan
JSPS15H00945 Japan
CitationJournal: Chem Asian J / Year: 2018
Title: Construction of a Triangle-Shaped Trimer and a Tetrahedron Using an alpha-Helix-Inserted Circular Permutant of Cytochrome c555.
Authors: Oda, A. / Nagao, S. / Yamanaka, M. / Ueda, I. / Watanabe, H. / Uchihashi, T. / Shibata, N. / Higuchi, Y. / Hirota, S.
History
DepositionDec 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Apr 4, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 22, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1483
Polymers10,3351
Non-polymers8132
Water1,53185
1
A: Cytochrome c552
hetero molecules

A: Cytochrome c552
hetero molecules

A: Cytochrome c552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4439
Polymers31,0053
Non-polymers2,4386
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation30_544z,-x-1/2,-y-1/21
crystal symmetry operation84_445-y-1/2,-z-1/2,x1
Buried area11470 Å2
ΔGint-134 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.804, 153.804, 153.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-284-

HOH

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Components

#1: Protein Cytochrome c552


Mass: 10335.003 Da / Num. of mol.: 1 / Mutation: K45A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: cycB2, aq_1550 / Production host: Escherichia coli (E. coli) / Strain (production host): JCB387 / References: UniProt: O67504
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.67 Å3/Da / Density % sol: 66.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0 M ammonium sulfate with 2% (v/v) PEG 400, 100 mM HEPES buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 19058 / % possible obs: 96 % / Redundancy: 18.6 % / Net I/σ(I): 23.839
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 1005 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2zxy

2zxy


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.726 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.11 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26831 881 5.2 %RANDOM
Rwork0.22693 ---
obs0.22905 15942 94.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.177 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms723 0 56 85 864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.019793
X-RAY DIFFRACTIONr_bond_other_d0.0020.02799
X-RAY DIFFRACTIONr_angle_refined_deg2.1582.0781074
X-RAY DIFFRACTIONr_angle_other_deg0.89931845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.706595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83627.58629
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15915144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.379151
X-RAY DIFFRACTIONr_chiral_restr0.0620.2112
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021889
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02156
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_it1.2311.757383
X-RAY DIFFRACTIONr_mcbond_other1.231.757382
X-RAY DIFFRACTIONr_mcangle_it1.6752.642477
X-RAY DIFFRACTIONr_mcangle_other1.6742.642478
X-RAY DIFFRACTIONr_scbond_it1.6512.025410
X-RAY DIFFRACTIONr_scbond_other1.652.025410
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0062.883598
X-RAY DIFFRACTIONr_long_range_B_refined2.88214.578982
X-RAY DIFFRACTIONr_long_range_B_other2.51314.196952
X-RAY DIFFRACTIONr_rigid_bond_restr1.84631592
X-RAY DIFFRACTIONr_sphericity_free28.913531
X-RAY DIFFRACTIONr_sphericity_bonded7.73251632
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 68 -
Rwork0.205 1213 -
obs--100 %

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