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- PDB-3fvb: Crystal structure of ferritin (bacterioferritin) from Brucella me... -

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Basic information

Entry
Database: PDB / ID: 3fvb
TitleCrystal structure of ferritin (bacterioferritin) from Brucella melitensis
ComponentsBacterioferritin
KeywordsMETAL BINDING PROTEIN / NIAID / SSGCID / deCODE / ferritin / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis
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 / IMIDAZOLE / Bacterioferritin
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus 2308 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.806 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of ferritin from Brucella melitensis
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJan 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: 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 / struct_conn / struct_ref_seq_dif / 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_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_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_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.pdbx_dist_value / _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_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,96018
Polymers41,7632
Non-polymers1,19716
Water6,612367
1
A: Bacterioferritin
B: Bacterioferritin
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)515,522216
Polymers501,15424
Non-polymers14,368192
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation16_544x,-y-1/2,-z-1/21
crystal symmetry operation20_544-z,x-1/2,-y-1/21
crystal symmetry operation24_544-y,-z-1/2,x-1/21
crystal symmetry operation27_554-x+1/2,y,-z-1/21
crystal symmetry operation30_554z+1/2,-x,-y-1/21
crystal symmetry operation33_554y+1/2,z,x-1/21
crystal symmetry operation38_545-x+1/2,-y-1/2,z1
crystal symmetry operation41_545z+1/2,x-1/2,y1
crystal symmetry operation47_545y+1/2,-z-1/2,-x1
Buried area105640 Å2
ΔGint-1033 kcal/mol
Surface area128340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.810, 174.810, 174.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-167-

MG

21A-168-

NA

31A-169-

CL

41A-170-

CL

51B-166-

CL

61A-242-

HOH

71A-291-

HOH

81B-267-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bacterioferritin /


Mass: 20881.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Expressed as a N-terminal hexahis tag with 3C protease cleavage site. Fusion tag was not cleaved prior to crystallization.
Source: (gene. exp.) Brucella melitensis biovar Abortus 2308 (bacteria)
Strain: biovar Abortus 2308 / Gene: bfr, BAB2_0675 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YKI4

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Non-polymers , 7 types, 383 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12.4 mg/mL protein, 30% PEG 400, 0.2 M MGCl2, 0.1 M HEPES pH 7.5, 0.1 M imidazole; Crystal ID 200992h8. Original crystal hit was in JCSG+ D2, which was optimized using the Emerald Biosystems ...Details: 12.4 mg/mL protein, 30% PEG 400, 0.2 M MGCl2, 0.1 M HEPES pH 7.5, 0.1 M imidazole; Crystal ID 200992h8. Original crystal hit was in JCSG+ D2, which was optimized using the Emerald Biosystems ADDit Additive Screen. , VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 40564 / % possible obs: 100 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.081 / Χ2: 1.151 / Net I/σ(I): 26.769
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.868.20.84340640.76399.8
1.86-1.948.40.59940040.803100
1.94-2.038.30.41840270.879100
2.03-2.138.30.27740281.045100
2.13-2.278.30.20340351.175100
2.27-2.448.50.15440481.324100
2.44-2.699.10.11940421.403100
2.69-3.0810.20.09140641.7100
3.08-3.8811.20.05940841.326100
3.88-5011.10.03941680.93199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.5.0053refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JGC, molecule A

1jgc


Resolution: 1.806→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.176 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 2.149 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY; CHLORIDE IONS MIGHT BE OTHER NEGATIVELY CHARGED IONS SUCH AS PHOSPHATE OR SULFATE, BUT CHLORIDE IONS ARE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY; CHLORIDE IONS MIGHT BE OTHER NEGATIVELY CHARGED IONS SUCH AS PHOSPHATE OR SULFATE, BUT CHLORIDE IONS ARE MOST LIKELY GIVEN CRYSTALLANT COMPOSITION
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2028 5 %RANDOM
Rwork0.181 ---
obs0.183 40464 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.17 Å2 / Biso mean: 25.375 Å2 / Biso min: 16.08 Å2
Refinement stepCycle: LAST / Resolution: 1.806→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 65 367 3024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222700
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9993641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2155320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68424.965143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54515484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2221518
X-RAY DIFFRACTIONr_chiral_restr0.0840.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022082
X-RAY DIFFRACTIONr_mcbond_it0.661.51592
X-RAY DIFFRACTIONr_mcangle_it1.34922531
X-RAY DIFFRACTIONr_scbond_it2.78131108
X-RAY DIFFRACTIONr_scangle_it4.9664.51110
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.806-1.8530.291460.2362796295099.729
1.853-1.9030.2511500.19927852935100
1.903-1.9590.2331450.2042664281099.964
1.959-2.0190.2451440.19526072751100
2.019-2.0850.2241320.1882491262499.962
2.085-2.1580.2231250.1712471259999.885
2.158-2.240.2141180.1772355247699.879
2.24-2.3310.251230.1772294241899.959
2.331-2.4350.2181120.1782158228199.518
2.435-2.5530.211020.1862087219599.727
2.553-2.6910.2391050.1841985209499.809
2.691-2.8550.246970.1861877198499.496
2.855-3.0510.228950.1821764186399.785
3.051-3.2960.204800.1911656174099.77
3.296-3.610.181670.1571524159399.874
3.61-4.0350.18810.1551379146399.795
4.035-4.6580.166690.151226129799.846
4.658-5.7020.199530.1910371090100
5.702-8.0510.281640.231803867100
8.051-101.0150.165200.2147750698.221

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