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- PDB-4tof: 1.65A resolution structure of BfrB (C89S, K96C) crystal form 1 fr... -

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Basic information

Entry
Database: PDB / ID: 4tof
Title1.65A resolution structure of BfrB (C89S, K96C) crystal form 1 from Pseudomonas aeruginosa
ComponentsBacterioferritin
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / IRON STORAGE / iron binding / iron mobilization
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / 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 BfrB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsLovell, S. / Battaile, K.P. / Yao, H. / Kumar, R. / Eshelman, K. / Rivera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1158469 United States
CitationJournal: Biochemistry / Year: 2015
Title: Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic.
Authors: Yao, H. / Rui, H. / Kumar, R. / Eshelman, K. / Lovell, S. / Battaile, K.P. / Im, W. / Rivera, M.
History
DepositionJun 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / refine_hist / struct_conn
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.ptnr1_symmetry / _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_alt_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.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,55124
Polymers74,1524
Non-polymers3,39920
Water13,727762
1
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)465,305144
Polymers444,91424
Non-polymers20,392120
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
crystal symmetry operation11_554-x+y,y,-z-1/21
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area97700 Å2
ΔGint-1394 kcal/mol
Surface area130840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.568, 158.568, 152.381
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11C-201-

HEM

21C-201-

HEM

31D-201-

HEM

41D-201-

HEM

51D-201-

HEM

61B-329-

HOH

71B-334-

HOH

81B-335-

HOH

DetailsThe biological unit (24-mer) can be generated by applying the following symmetry operators on the asymmetric unit: -X+Y, Y, -Z-1/2 -Y-1, X-Y-1, Z -Y-1, -X-1, -Z-1/2 -X+Y, -X-1, Z X, X-Y-1, -Z-1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Bacterioferritin


Mass: 18538.066 Da / Num. of mol.: 4 / Mutation: C89S, K96C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: bfrB, PA3531 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): ARCTIC EXPRESS RIL / References: UniProt: Q9HY79, ferroxidase

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Non-polymers , 5 types, 782 molecules

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


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / 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

CrystalColour: Red Prism / Density Matthews: 3.73 Å3/Da / Density % sol: 67.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 35% (v/v) MPD, 0.1M MES, 0.2M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→49.13 Å / Num. obs: 134788 / % possible obs: 100 % / Redundancy: 19.9 % / Biso Wilson estimate: 20.67 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.039 / Net I/σ(I): 12.3 / Num. measured all: 2688900 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.65-1.6820.31.8342.313446066100.7830.41299.9
9.04-49.1317.90.10529.1175159770.9880.02599.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
XDSdata scaling
PHASERphasing
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IS7

3is7


Resolution: 1.65→38.095 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.69 / Phase error: 15.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1621 6770 5.03 %
Rwork0.1451 127956 -
obs0.146 134726 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.21 Å2 / Biso mean: 22.5906 Å2 / Biso min: 11.65 Å2
Refinement stepCycle: final / Resolution: 1.65→38.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5117 0 273 762 6152
Biso mean--30.94 33.97 -
Num. residues----628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085527
X-RAY DIFFRACTIONf_angle_d1.1077530
X-RAY DIFFRACTIONf_chiral_restr0.043802
X-RAY DIFFRACTIONf_plane_restr0.005945
X-RAY DIFFRACTIONf_dihedral_angle_d18.1312044
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.65-1.66880.23622130.227642204433
1.6688-1.68840.25292280.217642084436
1.6884-1.7090.23352250.204642034428
1.709-1.73060.20682160.201342084424
1.7306-1.75340.24312230.19342234446
1.7534-1.77740.20822180.182842134431
1.7774-1.80280.21572050.185242414446
1.8028-1.82970.20262230.178741804403
1.8297-1.85830.1832450.172642274472
1.8583-1.88880.17412210.173142064427
1.8888-1.92130.18122220.164742284450
1.9213-1.95630.17992400.16142164456
1.9563-1.99390.1812370.149542094446
1.9939-2.03460.1782170.149142564473
2.0346-2.07880.1752040.142842334437
2.0788-2.12720.1552110.139942554466
2.1272-2.18040.15522070.133442614468
2.1804-2.23930.15072270.133742304457
2.2393-2.30520.15992500.130142484498
2.3052-2.37960.1571950.130842604455
2.3796-2.46460.15412170.124442804497
2.4646-2.56330.14532220.124942844506
2.5633-2.67990.14562490.135442444493
2.6799-2.82120.16372300.144542904520
2.8212-2.99780.15252360.142342804516
2.9978-3.22920.17022440.150943094553
3.2292-3.5540.16032370.141343144551
3.554-4.06770.13722280.128843734601
4.0677-5.12290.11962250.121644294654
5.1229-38.10540.1812550.164446284883

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