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- PDB-1nfv: X-ray structure of Desulfovibrio desulfuricans bacterioferritin: ... -

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Basic information

Entry
Database: PDB / ID: 1nfv
TitleX-ray structure of Desulfovibrio desulfuricans bacterioferritin: the diiron centre in different catalytic states (as-isolated structure)
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


iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / heme binding / cytosol
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
3-HYDROXYPYRUVIC ACID / : / Chem-FEC / : / Bacterioferritin
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 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 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1May 2, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...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_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_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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
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)333,169132
Polymers318,50016
Non-polymers14,669116
Water34,0481890
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)498,925189
Polymers477,75124
Non-polymers21,175165
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
Buried area105400 Å2
ΔGint-512 kcal/mol
Surface area139540 Å2
MethodPISA, PQS
3
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)500,583207
Polymers477,75124
Non-polymers22,832183
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
Buried area109570 Å2
ΔGint-506 kcal/mol
Surface area138770 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)225.300, 225.300, 225.300
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

31J-1904-

SO4

41A-1210-

HOH

51A-1212-

HOH

61C-9737-

HOH

Detailsthe biologically relevant molecule is formed applying the following symmetry operations to chains A, B, G, H, I, J, M and N: -z, 1/2+x, 1/2-y and the combination of the three operations 1/2-z, -x, 1/2+y; z, x, y; x-1, y, z;

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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: GenBank: 14326006, UniProt: Q93PP9*PLUS

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Non-polymers , 6 types, 2006 molecules

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


Mass: 55.845 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Fe
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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
#6: Chemical ChemComp-3PY / 3-HYDROXYPYRUVIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1890 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1410.992, 1.7387, 1.74
SYNCHROTRONESRF ID14-220.933
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDSep 15, 1999collimating and focusing mirrors
ADSC QUANTUM 42CCDFeb 2, 2000toroidal mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) channel cutMADMx-ray1
2diamond (111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9921
21.73871
31.741
40.9331
ReflectionResolution: 1.95→30 Å / Num. all: 271259 / Num. obs: 271259 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 6.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.1 / % possible all: 97.6
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 905598
Reflection shell
*PLUS
% possible obs: 97.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
SnBphasing
MLPHAREphasing
DMmodel building
SHELXL-97refinement
CCP4(SCALA)data scaling
DMphasing
RefinementMethod to determine structure: MAD
Starting model: polyalanine model, built from scratch

Resolution: 1.95→30 Å / Num. restraintsaints: 327899 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: electron density above diiron site not modelled, seems to be a mixture of states
RfactorNum. reflection% reflectionSelection details
Rfree0.254 5260 -thin resolution shells
Rwork0.214 ---
obs0.214 265820 98.9 %-
all-265820 --
Displacement parametersBiso mean: 31.6 Å2
Refine analyzeOccupancy sum non hydrogen: 24247.95
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21300 0 829 1890 24019
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.031
X-RAY DIFFRACTIONs_from_restr_planes0.019
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.071
X-RAY DIFFRACTIONs_zero_chiral_vol0.025
LS refinement shellResolution: 1.95→2.02 Å /
RfactorNum. reflection
Rwork0.237 -
obs-26867
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 1.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.015

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