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- PDB-1nf6: X-ray structure of the Desulfovibrio desulfuricans bacterioferrit... -

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Basic information

Entry
Database: PDB / ID: 1nf6
TitleX-ray structure of the Desulfovibrio desulfuricans bacterioferritin: the diiron site in different catalytic states ("cycled" structure: reduced in solution and allowed to reoxidise before crystallisation)
Componentsbacterioferritin
KeywordsIRON STORAGE/ELECTRON TRANSPORT / bacterioferritin / 24 subunits in the active molecule / diiron centre / haem Fe-Coproporphyrin III cofactor / IRON STORAGE-ELECTRON TRANSPORT COMPLEX
Function / homology
Function and homology information


ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport
Similarity search - Function
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
: / Chem-FEC / Bacterioferritin
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / structure solved using the native as-isolated structure as starting model / Resolution: 2.35 Å
AuthorsMacedo, S. / Romao, C.V. / Mitchell, E. / Matias, P.M. / Liu, M.Y. / Xavier, A.V. / LeGall, J. / Teixeira, M. / Lindley, P. / Carrondo, M.A.
Citation
Journal: NAT.STRUCT.BIOL. / Year: 2003
Title: The nature of the di-iron site in the bacterioferritin from Desulfovibrio desulfuricans
Authors: Macedo, S. / Romao, C.V. / Mitchell, E. / Matias, P.M. / Liu, M.Y. / Xavier, A.V. / LeGall, J. / Teixeira, M. / Lindley, P. / Carrondo, M.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure determination of bacterioferritin from Desulfovibrio desulfuricans by the MAD method at the Fe K-edge
Authors: Coelho, A.V. / Macedo, S. / Matias, P.M. / Thompson, A.W. / LeGall, J. / Carrondo, M.A.
History
DepositionDec 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 3, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _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_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.ptnr2_auth_asym_id / _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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 350GENERATING THE BIOMOLECULE THE ACTIVE BIOLOGICAL UNIT IS A 24-MER. SINCE THE ASYMMETRIC UNIT ...GENERATING THE BIOMOLECULE THE ACTIVE BIOLOGICAL UNIT IS A 24-MER. SINCE THE ASYMMETRIC UNIT CONTAINS PARTS OF TWO DIFFERENT SPHERES, APPLY THE SYMMETRY OPERATIONS (-z, 1/2+x, 1/2-y) AND (y-1/2, 1/2-z, -x) TO MONOMERS A, B, G, H, I, J, M AND N OR THE SYMMETRY OPERATIONS (z+1/2, 1/2-x, -y) AND (1/2-y, -z, x-1/2) TO THE REMAINING MONOMERS IN THE ASYMMETRIC UNIT TO GENERATE THE 24-MER.

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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
M: bacterioferritin
N: bacterioferritin
O: bacterioferritin
P: bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)328,42175
Polymers318,50016
Non-polymers9,92059
Water32,6251811
1
A: bacterioferritin
B: bacterioferritin
G: bacterioferritin
H: bacterioferritin
I: bacterioferritin
J: bacterioferritin
M: bacterioferritin
N: bacterioferritin
hetero molecules

A: bacterioferritin
B: bacterioferritin
G: bacterioferritin
H: bacterioferritin
I: bacterioferritin
J: bacterioferritin
M: bacterioferritin
N: bacterioferritin
hetero molecules

A: bacterioferritin
B: bacterioferritin
G: bacterioferritin
H: bacterioferritin
I: bacterioferritin
J: bacterioferritin
M: bacterioferritin
N: bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)493,069117
Polymers477,75124
Non-polymers15,31893
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
MethodPQS
2
C: bacterioferritin
D: bacterioferritin
E: bacterioferritin
F: bacterioferritin
K: bacterioferritin
L: bacterioferritin
O: bacterioferritin
P: bacterioferritin
hetero molecules

C: bacterioferritin
D: bacterioferritin
E: bacterioferritin
F: bacterioferritin
K: bacterioferritin
L: bacterioferritin
O: bacterioferritin
P: bacterioferritin
hetero molecules

C: bacterioferritin
D: bacterioferritin
E: bacterioferritin
F: bacterioferritin
K: bacterioferritin
L: bacterioferritin
O: bacterioferritin
P: bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,193108
Polymers477,75124
Non-polymers14,44284
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
MethodPQS
3
M: bacterioferritin
N: bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,20911
Polymers39,8132
Non-polymers1,3979
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-109 kcal/mol
Surface area14900 Å2
MethodPISA
4
E: bacterioferritin
F: bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0179
Polymers39,8132
Non-polymers1,2047
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-84 kcal/mol
Surface area14760 Å2
MethodPISA
5
C: bacterioferritin
D: bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9218
Polymers39,8132
Non-polymers1,1086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-69 kcal/mol
Surface area14740 Å2
MethodPISA
6
I: bacterioferritin
J: bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,11310
Polymers39,8132
Non-polymers1,3018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-81 kcal/mol
Surface area14920 Å2
MethodPISA
7
K: bacterioferritin
L: bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,20911
Polymers39,8132
Non-polymers1,3979
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-93 kcal/mol
Surface area15050 Å2
MethodPISA
8
G: bacterioferritin
H: bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0179
Polymers39,8132
Non-polymers1,2047
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-96 kcal/mol
Surface area14990 Å2
MethodPISA
9
O: bacterioferritin
P: bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9178
Polymers39,8132
Non-polymers1,1046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-80 kcal/mol
Surface area14770 Å2
MethodPISA
10
A: bacterioferritin
B: bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0179
Polymers39,8132
Non-polymers1,2047
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-82 kcal/mol
Surface area14670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.790, 225.790, 225.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1004-

SO4

21A-1004-

SO4

31C-1304-

SO4

41C-1304-

SO4

51J-2004-

SO4

61J-2004-

SO4

71L-2204-

SO4

81L-2204-

SO4

91A-1104-

HOH

101A-1118-

HOH

111L-9608-

HOH

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Components

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Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP

#1: Protein
bacterioferritin /


Mass: 19906.281 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio desulfuricans (bacteria) / Strain: ATCC 27774 / References: UniProt: Q93PP9

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Non-polymers , 5 types, 1870 molecules

#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-FEC / 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX / FE-COPROPORPHYRIN III


Mass: 708.538 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C36H36FeN4O8
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1811 / 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: 2.29 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: ammonium sulfate, sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
pH: 3.6
Details: Coelho, A.V., (2001) Acta Crystallogr., Sect.D, 57, 326.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.0 Mammonium sulfate1reservoir
20.1 Macetate1reservoirpH3.6
313 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 18, 2001 / Details: toroidal mirrors
RadiationMonochromator: diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. all: 152336 / Num. obs: 152336 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 6.8
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 2.7 / Num. unique all: 15292 / % possible all: 99
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 477229
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
SHELXL-97refinement
SCALAdata scaling
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: structure solved using the native as-isolated structure as starting model
Starting model: as-isolated model for this protein; phases obtained by MAD at the iron K edge.

Resolution: 2.35→30 Å / Num. restraintsaints: 358918 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 3043 -thin resolution shells
Rwork0.197 ---
obs0.197 149010 96.5 %-
all-149010 --
Displacement parametersBiso mean: 28 Å2
Refine analyzeOccupancy sum non hydrogen: 23645.6
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21134 0 584 1811 23529
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.015
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.022
X-RAY DIFFRACTIONs_from_restr_planes0.016
LS refinement shellResolution: 2.35→2.44 Å /
RfactorNum. reflection
Rwork0.24 -
Rfree-324
obs-16219
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Lowest resolution: 2.43 Å / Rfactor Rfree: 0.02

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