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- PDB-4cvr: Structure of Apobacterioferritin Y25F variant -

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Basic information

Entry
Database: PDB / ID: 4cvr
TitleStructure of Apobacterioferritin Y25F variant
ComponentsBACTERIOFERRITIN
KeywordsOXIDOREDUCTASE / 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
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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)18,8735
Polymers18,6111
Non-polymers2624
Water3,441191
1
A: BACTERIOFERRITIN
hetero molecules

A: BACTERIOFERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,74610
Polymers37,2222
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3040 Å2
ΔGint-227 kcal/mol
Surface area16140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.380, 27.950, 56.710
Angle α, β, γ (deg.)90.00, 119.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2089-

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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 1.94 Å3/Da / Density % sol: 34.49 % / 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: 1.02→27.43 Å / Num. obs: 52678 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 2.58 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.91
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 1.69 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.74 / % possible all: 57.2

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Processing

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

2vxi


Resolution: 1.1→27.43 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.206 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.16544 2687 5.1 %RANDOM
Rwork0.13373 ---
obs0.13534 49990 91.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.109 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.25 Å2
2--1.55 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.1→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 4 191 1481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191325
X-RAY DIFFRACTIONr_bond_other_d0.0010.021285
X-RAY DIFFRACTIONr_angle_refined_deg1.9671.9761784
X-RAY DIFFRACTIONr_angle_other_deg0.93332952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9715161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12325.06775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14715262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0551511
X-RAY DIFFRACTIONr_chiral_restr0.1350.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021518
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02303
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_it2.6731.061635
X-RAY DIFFRACTIONr_mcbond_other2.5811.057634
X-RAY DIFFRACTIONr_mcangle_it3.2081.595796
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.611.541690
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr6.45732609
X-RAY DIFFRACTIONr_sphericity_free38.154537
X-RAY DIFFRACTIONr_sphericity_bonded13.15952748
LS refinement shellResolution: 1.104→1.133 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 111 -
Rwork0.266 2296 -
obs--56.8 %

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