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- PDB-4wgy: Crystal Structure of Cytochrome c' from Alcaligenes xylosoxidans ... -

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Basic information

Entry
Database: PDB / ID: 4wgy
TitleCrystal Structure of Cytochrome c' from Alcaligenes xylosoxidans NCIMB 11015 at pH 10.4
ComponentsCytochrome c'
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome c prime, subgroup / Cytochrome c prime / Cytochrome c class II profile. / Cytochrome c, class II / Cytochrome C' / Cytochrome c/b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c'
Similarity search - Component
Biological speciesAlcaligenes xylosoxydans xylosoxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsTakashina, A. / Unno, M. / Kohzuma, T.
CitationJournal: CHEM LETT. / Year: 2015
Title: X-ray Crystallographic Elucidation for the Alkaline High-spin State Transition of Iron(III) Cytochrome c' from Alcaligenes xylosoxidans NCIMB 11015
Authors: Takashina, A. / Unno, M. / Kohzuma, T.
History
DepositionSep 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 2.0Jan 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_poly / entity_src_nat / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2502
Polymers13,6311
Non-polymers6191
Water4,089227
1
A: Cytochrome c'
hetero molecules

A: Cytochrome c'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5004
Polymers27,2632
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area3590 Å2
ΔGint-52 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.666, 52.666, 183.584
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-378-

HOH

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Components

#1: Protein Cytochrome c'


Mass: 13631.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Alcaligenes xylosoxydans xylosoxydans (bacteria)
References: UniProt: P00138
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.4
Details: 24 % PEG4000, 100 mM CAPS, 50 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.75 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 26188 / % possible obs: 99.6 % / Redundancy: 20.8 % / Net I/σ(I): 64.1

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+83 / Resolution: 1.48→45.61 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.495 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17253 1328 5.1 %RANDOM
Rwork0.13833 ---
obs0.14002 24765 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.352 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.02 Å20 Å2
2---0.02 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.48→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 43 227 1214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0191079
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.772.0221481
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4295142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.58224.52442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64115182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.942155
X-RAY DIFFRACTIONr_chiral_restr0.1580.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.021841
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_it3.020.826527
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9231.239664
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5950.998552
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.4362047
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.02431079
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded7.93451042
LS refinement shellResolution: 1.482→1.521 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 70 -
Rwork0.12 1793 -
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: -16.084 Å / Origin y: 20.867 Å / Origin z: 10.056 Å
111213212223313233
T0.0214 Å2-0.0005 Å2-0.0011 Å2-0.0195 Å20.0038 Å2--0.0131 Å2
L0.0554 °20.0263 °20.0229 °2-0.0143 °20.009 °2--0.0164 °2
S-0.0022 Å °0.0022 Å °0.0084 Å °-0.003 Å °-0.0007 Å °0.0045 Å °-0.0049 Å °0.0025 Å °0.0029 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 126
2X-RAY DIFFRACTION1A201

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