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- PDB-4cvs: Structure of Apobacterioferritin Y45F variant -

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Basic information

Entry
Database: PDB / ID: 4cvs
TitleStructure of Apobacterioferritin Y45F variant
ComponentsBACTERIOFERRITIN
KeywordsOXIDOREDUCTASE / FERRITIN / ELECTRON TRANSFER
Function / homology
Function and homology information


iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity ...iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity / identical protein binding / membrane / cytosol
Similarity search - Function
Bacterioferritin signature. / Bacterioferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Bacterioferritin signature. / Bacterioferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Bacterioferritin
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.392 Å
AuthorsHingorani, K. / Pace, R. / Whitney, S. / Murray, J.W. / Wydrzynski, T. / Cheah, M.H. / Smith, P. / Hillier, W.
CitationJournal: Biochim.Biophys.Acta / Year: 2014
Title: Photo-Oxidation of Tyrosine in a Bio-Engineered Bacterioferritin 'Reaction Centre'-A Protein Model for Artificial Photosynthesis.
Authors: Hingorani, K. / Pace, R. / Whitney, S. / Murray, J.W. / Smith, P. / Cheah, M.H. / Wydrzynski, T. / Hillier, W.
History
DepositionMar 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BACTERIOFERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9484
Polymers18,6111
Non-polymers3373
Water2,612145
1
A: BACTERIOFERRITIN
hetero molecules

A: BACTERIOFERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8978
Polymers37,2222
Non-polymers6746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2990 Å2
ΔGint-60.7 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.490, 27.840, 56.760
Angle α, β, γ (deg.)90.00, 119.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2067-

HOH

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Components

#1: Protein BACTERIOFERRITIN / BFR / CYTOCHROME B-1 / CYTOCHROME B-557 / FERRITIN


Mass: 18611.188 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0ABD3, ferroxidase
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 1.92 Å3/Da / Density % sol: 35.87 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0077
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0077 Å / Relative weight: 1
ReflectionResolution: 1.39→49.56 Å / Num. obs: 26385 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.63 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.32
Reflection shellResolution: 1.39→1.4 Å / Redundancy: 1.79 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.02 / % possible all: 74.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
TRUNCATEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VXI

2vxi


Resolution: 1.392→49.557 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.915 / SU B: 1.432 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rfree0.2249 1337 5.17 %
Rwork0.203 --
obs0.204 26384 91.707 %
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.712 Å2
Baniso -1Baniso -2Baniso -3
1--0.546 Å20 Å2-0.398 Å2
2--2.394 Å20 Å2
3----0.864 Å2
Refinement stepCycle: LAST / Resolution: 1.392→49.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1291 0 3 145 1439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191312
X-RAY DIFFRACTIONr_bond_other_d0.0010.021282
X-RAY DIFFRACTIONr_angle_refined_deg1.8921.9771763
X-RAY DIFFRACTIONr_angle_other_deg0.84332941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05624.93273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83915260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4491511
X-RAY DIFFRACTIONr_chiral_restr0.1080.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021489
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02300
X-RAY DIFFRACTIONr_nbd_refined0.2530.2497
X-RAY DIFFRACTIONr_nbd_other0.190.250
X-RAY DIFFRACTIONr_nbtor_refined0.1910.2661
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0540.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0810.23
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_refined0.0590.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.561.414629
X-RAY DIFFRACTIONr_mcbond_other1.5481.409628
X-RAY DIFFRACTIONr_mcangle_it2.422.113785
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3951.706683
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7192.436977
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.392→1.428 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 79 -
Rwork0.254 1437 -
obs--73.7 %

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