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- PDB-3isf: Structure of non-mineralized Bfrb (as-isolated) from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 3isf
TitleStructure of non-mineralized Bfrb (as-isolated) from Pseudomonas aeruginosa to 2.07A Resolution
ComponentsBacterioferritin
KeywordsELECTRON TRANSPORT / iron storage / Heme / Iron / Metal-binding
Function / homology
Function and homology information


ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / iron ion binding / heme binding / 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 speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.07 Å
AuthorsLovell, S. / Weeratunga, S.K. / Battaile, K.P. / Rivera, M.
CitationJournal: Biochemistry / Year: 2010
Title: Structural Studies of Bacterioferritin B from Pseudomonas aeruginosa Suggest a Gating Mechanism for Iron Uptake via the Ferroxidase Center
Authors: Weeratunga, S.K. / Lovell, S. / Yao, H. / Battaile, K.P. / Fischer, C.J. / Gee, C.E. / Rivera, M.
History
DepositionAug 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: 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 / pdbx_struct_special_symmetry / struct_conn / 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,02512
Polymers111,4816
Non-polymers2,5446
Water6,539363
1
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
hetero molecules

A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
hetero molecules

A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
hetero molecules

A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)456,10148
Polymers445,92424
Non-polymers10,17724
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
MethodPISA
Unit cell
Length a, b, c (Å)122.761, 126.274, 168.553
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-159-

K

21E-159-

HEM

31E-159-

HEM

41F-159-

HEM

51F-159-

HEM

DetailsThe biological assembly is a 24-mer generated from chains A, B, C, D, E, F by the operations: x, -y+1, -z; -x -y+1, z; -x, -y, z

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Components

#1: Protein
Bacterioferritin


Mass: 18580.168 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bfrB, PA3531 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic express RIL / References: UniProt: Q9HY79
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 58.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: 35% MPD, 100mM TRIS, 200mM ammonium sulfate, pH 8.5, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1.6531 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 15, 2009
Diffraction measurementDetails: 1.00 degrees, 20.0 sec, detector distance 100.00 mm
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6531 Å / Relative weight: 1
ReflectionAv R equivalents: 0.09 / Number: 550910
ReflectionResolution: 2.07→44.02 Å / Num. obs: 79588 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 20.279
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.375 / Num. unique all: 7764 / Rsym value: 0.504 / % possible all: 97.8
Cell measurementReflection used: 550910

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.39 Å44.01 Å
Translation2.39 Å44.01 Å

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0066refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IS7

3is7


Resolution: 2.07→44.02 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.18 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.441 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3973 5 %RANDOM
Rwork0.198 ---
obs0.2 79324 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 71.76 Å2 / Biso mean: 38.903 Å2 / Biso min: 19.95 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å20 Å2
2---0.54 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.07→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7703 0 174 363 8240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0218034
X-RAY DIFFRACTIONr_bond_other_d00.027214
X-RAY DIFFRACTIONr_angle_refined_deg1.8712.03310873
X-RAY DIFFRACTIONr_angle_other_deg0.889316877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2655937
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85625.877422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.042151566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.2731530
X-RAY DIFFRACTIONr_chiral_restr0.1370.21166
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028772
X-RAY DIFFRACTIONr_gen_planes_other00.021406
X-RAY DIFFRACTIONr_mcbond_it0.9131.54626
X-RAY DIFFRACTIONr_mcbond_other0.2771.51931
X-RAY DIFFRACTIONr_mcangle_it1.64527421
X-RAY DIFFRACTIONr_scbond_it2.95233408
X-RAY DIFFRACTIONr_scangle_it4.6244.53447
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 (%)
2.07-2.1240.3142850.2415408581897.851
2.124-2.1820.2962750.2265336568798.664
2.182-2.2450.2652770.2265213553499.205
2.245-2.3140.3142590.245069538398.978
2.314-2.390.2612320.2094956522599.292
2.39-2.4730.2332360.1884780503499.642
2.473-2.5660.2682410.214607486899.589
2.566-2.6710.2452830.2044427472199.767
2.671-2.7890.2722120.2084290450999.845
2.789-2.9250.2692090.24104431699.93
2.925-3.0830.2621760.2173933411199.951
3.083-3.2690.2582010.2113708391399.898
3.269-3.4930.2412060.1923460367399.809
3.493-3.7720.231780.17732323410100
3.772-4.1290.1911580.1593002317099.685
4.129-4.6130.1861480.1392739289199.862
4.613-5.3190.2171400.17824212561100
5.319-6.4960.2771110.24820652176100
6.496-9.110.2371020.2131616172099.884
9.11-500.248440.222985103999.038

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