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- PDB-2vxi: The binding of heme and zinc in Escherichia coli Bacterioferritin -

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Basic information

Entry
Database: PDB / ID: 2vxi
TitleThe binding of heme and zinc in Escherichia coli Bacterioferritin
ComponentsBACTERIOFERRITIN
KeywordsMETAL TRANSPORT / BACTERIOFERRITIN / IRON STORAGE AND ELECTRON TRANSPORT / ZINC / HEME / IRON / IRON STORAGE / METAL-BINDING
Function / homology
Function and homology information


iron ion sequestering activity / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity ...iron ion sequestering activity / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / 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
PROTOPORPHYRIN IX CONTAINING FE / Bacterioferritin
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsWillies, S.C. / Isupov, M.N. / Garman, E.F. / Littlechild, J.A.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2009
Title: The Binding of Haem and Zinc in the 1.9 A X-Ray Structure of Escherichia Coli Bacterioferritin.
Authors: Willies, S.C. / Isupov, M.N. / Garman, E.F. / Littlechild, J.A.
History
DepositionJul 4, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id / _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

Downloads & links

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Assembly

Deposited unit
A: BACTERIOFERRITIN
B: BACTERIOFERRITIN
C: BACTERIOFERRITIN
D: BACTERIOFERRITIN
E: BACTERIOFERRITIN
F: BACTERIOFERRITIN
G: BACTERIOFERRITIN
H: BACTERIOFERRITIN
I: BACTERIOFERRITIN
J: BACTERIOFERRITIN
K: BACTERIOFERRITIN
L: BACTERIOFERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,97077
Polymers222,21612
Non-polymers11,75365
Water39,7772208
1
A: BACTERIOFERRITIN
B: BACTERIOFERRITIN
C: BACTERIOFERRITIN
D: BACTERIOFERRITIN
E: BACTERIOFERRITIN
F: BACTERIOFERRITIN
G: BACTERIOFERRITIN
H: BACTERIOFERRITIN
I: BACTERIOFERRITIN
J: BACTERIOFERRITIN
K: BACTERIOFERRITIN
L: BACTERIOFERRITIN
hetero molecules

A: BACTERIOFERRITIN
B: BACTERIOFERRITIN
C: BACTERIOFERRITIN
D: BACTERIOFERRITIN
E: BACTERIOFERRITIN
F: BACTERIOFERRITIN
G: BACTERIOFERRITIN
H: BACTERIOFERRITIN
I: BACTERIOFERRITIN
J: BACTERIOFERRITIN
K: BACTERIOFERRITIN
L: BACTERIOFERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)467,939154
Polymers444,43224
Non-polymers23,507130
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area96040 Å2
ΔGint-228.4 kcal/mol
Surface area167620 Å2
MethodPQS
Unit cell
Length a, b, c (Å)208.100, 208.100, 142.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11G-2182-

HOH

21G-2185-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.49894, -0.49874, 0.70875), (-0.49882, -0.50349, -0.70546), (0.70869, -0.70552, 0.00242)154.38416, 262.20419, 75.37856
2given(-0.49964, -0.50173, -0.70613), (0.50359, 0.49502, -0.70806), (0.70481, -0.70938, 0.00533)154.87177, 53.96763, 76.23669
3given(0.00413, 0.99999, 0.00283), (-0.99997, 0.00411, 0.00694), (0.00693, -0.00286, 0.99997)-107.59037, 207.42947, 0.05497
4given(-0.50123, 0.50117, 0.70541), (-0.50037, 0.49723, -0.7088), (-0.70597, -0.70824, 0.00154)-3.13047, 104.5271, 147.44206
5given(0.49985, -0.50138, -0.70624), (-0.50004, 0.49873, -0.70797), (0.70719, 0.70703, -0.00142)104.23199, 4.27228, -147.07896
6given(0.49666, -0.50422, -0.70646), (0.50062, -0.49848, 0.70774), (-0.70901, -0.70518, 0.00485)104.87283, 210.91911, 146.85373
7given(-0.49825, 0.50389, 0.70558), (0.50092, -0.49694, 0.70861), (0.70769, 0.70651, -0.00481)-3.72416, 210.6563, -147.23083
8given(0.506, 0.49482, 0.70648), (-0.49944, -0.49971, 0.70771), (0.70322, -0.71095, -0.00572)-53.26415, 261.79407, 76.71896
9given(-0.00275, -0.99999, 0.00459), (1, -0.00275, 0.00095), (-0.00094, 0.00459, 0.99999)208.34253, 107.55334, -0.62677
10given(-0.99996, 0.00631, 0.00562), (-0.00629, -0.99998, 0.0022), (0.00563, 0.00216, 0.99998)99.97652, 315.86658, -0.62382
11given(0.50374, 0.49628, -0.70707), (0.50625, 0.49362, 0.70714), (0.69997, -0.71417, -0.00259)-53.45027, 54.02396, 77.42868

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Components

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


Mass: 18518.016 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: BL21 / References: UniProt: P0ABD3
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2208 / 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: 2.93 Å3/Da / Density % sol: 57.74 % / Description: NONE
Crystal growpH: 7.5 / Details: 60% AMSO4, 20MM TRIS-HCL PH7.5, 0.1M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.739, 1.729
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 17, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.7391
21.7291
ReflectionResolution: 1.9→25 Å / Num. obs: 460546 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.77 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.14 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMACmodel building
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
DMphasing
REFMACphasing
REFMAC5.4.0057refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.91→147.44 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21561 4739 2 %RANDOM
Rwork0.17851 ---
obs0.17925 231295 98.68 %-
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: 24.852 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.91→147.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15528 0 685 2208 18421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02117032
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7042.0723087
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.72252002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9725.165939
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.743153186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.44315119
X-RAY DIFFRACTIONr_chiral_restr0.1180.22360
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213043
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_it2.55849498
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.184615254
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.57387534
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.676107767
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: 1.907→1.957 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.423 319
Rwork0.349 15365

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