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- PDB-4tob: 1.95A resolution structure of BfrB (Q151L) from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4tob
Title1.95A resolution structure of BfrB (Q151L) from Pseudomonas aeruginosa
ComponentsBacterioferritin
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / IRON STORAGE / iron binding / iron mobilization
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: 1.95 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 / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 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 / diffrn_radiation_wavelength / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
M: Bacterioferritin
N: Bacterioferritin
O: Bacterioferritin
P: Bacterioferritin
Q: Bacterioferritin
R: Bacterioferritin
S: Bacterioferritin
T: Bacterioferritin
U: Bacterioferritin
V: Bacterioferritin
W: Bacterioferritin
X: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)457,64860
Polymers445,56524
Non-polymers12,08436
Water54,0092998
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90490 Å2
ΔGint-515 kcal/mol
Surface area128760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.669, 203.154, 207.792
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H
91chain I
101chain J
111chain K
121chain L
131chain M
141chain N
151chain O
161chain P
171chain Q
181chain R
191chain S
201chain T
211chain U
221chain V
231chain W
241chain X

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1METMETGLUGLUchain AAA1 - 1561 - 156
2LYSLYSGLUGLUchain BBB2 - 1562 - 156
3LYSLYSGLUGLUchain CCC2 - 1562 - 156
4LYSLYSGLUGLUchain DDD2 - 1562 - 156
5LYSLYSGLUGLUchain EEE2 - 1562 - 156
6LYSLYSASPASPchain FFF2 - 1572 - 157
7LYSLYSGLUGLUchain GGG2 - 1562 - 156
8LYSLYSGLUGLUchain HHH2 - 1562 - 156
9LYSLYSGLUGLUchain III2 - 1562 - 156
10LYSLYSGLUGLUchain JJJ2 - 1562 - 156
11LYSLYSGLUGLUchain KKK2 - 1562 - 156
12GLYGLYGLUGLUchain LLL3 - 1563 - 156
13GLYGLYGLUGLUchain MMM3 - 1563 - 156
14METMETGLUGLUchain NNN1 - 1561 - 156
15LYSLYSGLUGLUchain OOO2 - 1562 - 156
16LYSLYSGLUGLUchain PPP2 - 1562 - 156
17GLYGLYGLUGLUchain QQQ3 - 1563 - 156
18LYSLYSGLUGLUchain RRR2 - 1562 - 156
19LYSLYSGLUGLUchain SSS2 - 1562 - 156
20LYSLYSGLUGLUchain TTT2 - 1562 - 156
21GLYGLYGLUGLUchain UUU3 - 1563 - 156
22LYSLYSGLUGLUchain VVV2 - 1562 - 156
23LYSLYSASPASPchain WWW2 - 1572 - 157
24LYSLYSGLUGLUchain XXX2 - 1562 - 156
DetailsThe asymmetric unit contains one biological unit

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Components

#1: Protein ...
Bacterioferritin


Mass: 18565.197 Da / Num. of mol.: 24 / Mutation: Q151L
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
#2: Chemical...
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2998 / 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: 2.98 Å3/Da / Density % sol: 58.68 %
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: Jul 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→49.34 Å / Num. obs: 384285 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 19.24 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.059 / Net I/σ(I): 10.8 / Num. measured all: 2639550 / Scaling rejects: 1
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
1.95-1.986.40.9582.2121492188630.6950.409100
10.68-49.346.50.05229.91655825650.9960.02298.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
XDSdata scaling
Cootmodel building
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: dev_1450)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→49.34 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 17.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1881 19327 5.03 %
Rwork0.1563 364760 -
obs0.1579 384087 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.82 Å2 / Biso mean: 20.873 Å2 / Biso min: 8.43 Å2
Refinement stepCycle: final / Resolution: 1.95→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30252 0 804 2998 34054
Biso mean--24.41 29.54 -
Num. residues----3720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00931644
X-RAY DIFFRACTIONf_angle_d1.00842862
X-RAY DIFFRACTIONf_chiral_restr0.0454656
X-RAY DIFFRACTIONf_plane_restr0.0065434
X-RAY DIFFRACTIONf_dihedral_angle_d17.02411834
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A23022X-RAY DIFFRACTION4.193TORSIONAL
12B23022X-RAY DIFFRACTION4.193TORSIONAL
13C23022X-RAY DIFFRACTION4.193TORSIONAL
14D23022X-RAY DIFFRACTION4.193TORSIONAL
15E23022X-RAY DIFFRACTION4.193TORSIONAL
16F23022X-RAY DIFFRACTION4.193TORSIONAL
17G23022X-RAY DIFFRACTION4.193TORSIONAL
18H23022X-RAY DIFFRACTION4.193TORSIONAL
19I23022X-RAY DIFFRACTION4.193TORSIONAL
110J23022X-RAY DIFFRACTION4.193TORSIONAL
111K23022X-RAY DIFFRACTION4.193TORSIONAL
112L23022X-RAY DIFFRACTION4.193TORSIONAL
113M23022X-RAY DIFFRACTION4.193TORSIONAL
114N23022X-RAY DIFFRACTION4.193TORSIONAL
115O23022X-RAY DIFFRACTION4.193TORSIONAL
116P23022X-RAY DIFFRACTION4.193TORSIONAL
117Q23022X-RAY DIFFRACTION4.193TORSIONAL
118R23022X-RAY DIFFRACTION4.193TORSIONAL
119S23022X-RAY DIFFRACTION4.193TORSIONAL
120T23022X-RAY DIFFRACTION4.193TORSIONAL
121U23022X-RAY DIFFRACTION4.193TORSIONAL
122V23022X-RAY DIFFRACTION4.193TORSIONAL
123W23022X-RAY DIFFRACTION4.193TORSIONAL
124X23022X-RAY DIFFRACTION4.193TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.97220.27896470.23311208512732100
1.9722-1.99540.26176360.22141207412710100
1.9954-2.01970.25676290.20791204412673100
2.0197-2.04530.23286670.19341205312720100
2.0453-2.07220.23166350.18741205712692100
2.0722-2.10060.22736020.18441214012742100
2.1006-2.13060.21866860.17531204512731100
2.1306-2.16240.21346560.16321206912725100
2.1624-2.19620.21316220.15551203712659100
2.1962-2.23220.18916600.15271213912799100
2.2322-2.27070.19856450.15361206112706100
2.2707-2.31190.18546270.14571211612743100
2.3119-2.35640.1926440.1471209212736100
2.3564-2.40450.17725650.14071214512710100
2.4045-2.45680.16666490.13891213212781100
2.4568-2.51390.18096590.13971210812767100
2.5139-2.57680.19816670.1491207712744100
2.5768-2.64650.1846440.14641211512759100
2.6465-2.72430.19626100.15391219612806100
2.7243-2.81230.19716790.15391207912758100
2.8123-2.91280.17746170.14231220412821100
2.9128-3.02940.1876420.15621215812800100
3.0294-3.16720.2026570.16211218312840100
3.1672-3.33420.18676360.15881220812844100
3.3342-3.5430.17276520.15751219212844100
3.543-3.81650.17917240.14711218412908100
3.8165-4.20040.15626500.13561227412924100
4.2004-4.80770.14836200.12391234712967100
4.8077-6.05550.186400.16771242913069100
6.0555-49.3520.17626600.1786127171337799

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