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- PDB-6p8l: Escherichia coli Bacterioferritin Substituted with Zinc Protoporp... -

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Basic information

Entry
Database: PDB / ID: 6p8l
TitleEscherichia coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (Zn Absorption Edge X-ray Data)
ComponentsBacterioferritin
KeywordsMETAL BINDING PROTEIN / OXIDOREDUCTASE / bacterioferritin / zinc protoporphyrin IX / photosensitizer / ferritin
Function / homology
Function and homology information


ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity / identical protein binding ...ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity / identical protein binding / membrane / 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
MALONATE ION / PROTOPORPHYRIN IX CONTAINING ZN / Bacterioferritin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsTaylor, A.B. / Cioloboc, D. / Kurtz, D.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)8UL1TR001120 United States
CitationJournal: Biochemistry / Year: 2020
Title: Structure of a Zinc Porphyrin-Substituted Bacterioferritin and Photophysical Properties of Iron Reduction.
Authors: Benavides, B.S. / Valandro, S. / Cioloboc, D. / Taylor, A.B. / Schanze, K.S. / Kurtz Jr., D.M.
History
DepositionJun 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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_validate_chiral / 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_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.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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,70762
Polymers222,21612
Non-polymers7,49050
Water28,7341595
1
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
hetero molecules

A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)459,413124
Polymers444,43224
Non-polymers14,981100
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area104270 Å2
ΔGint-356 kcal/mol
Surface area127460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.918, 207.918, 143.046
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-202-

NA

21F-203-

NA

31C-331-

HOH

41F-417-

HOH

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Bacterioferritin / BFR / Cytochrome b-1 / Cytochrome b-557


Mass: 18518.016 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: bfr, b3336, JW3298 / Plasmid: pCV3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABD3, ferroxidase

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Non-polymers , 5 types, 1645 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 102.046 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical
ChemComp-ZNH / PROTOPORPHYRIN IX CONTAINING ZN


Mass: 626.051 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32N4O4Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1595 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.49 Å3/Da / Density % sol: 64.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 2.4 M sodium malonate, pH 6.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C11.2822
SYNCHROTRONAPS 24-ID-C21.319
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELFeb 2, 2018
DECTRIS PILATUS 6M-F2PIXELFeb 2, 2018
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Cryo-cooled double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Cryo-cooled double crystal Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.28221
21.3191
Reflection

Entry-ID: 6P8L / CC1/2: 0.998 / % possible obs: 99.8 %

Resolution (Å)Num. obsRedundancy (%)Biso Wilson estimate (Å2)Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
2.1-92.651792577.330.160.1690.0670.18218.2
2.5-92.981079267.20.1770.0710.19128.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
2.1-2.217.51.7771.1258790.6990.9721.908199.9
2.5-2.647.21.7811.2155630.7370.7121.92299.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHENIX1.15.2_3472phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 6P8K

6p8k


Resolution: 2.1→92.65 Å / SU ML: 0.2974 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 31.7513
RfactorNum. reflection% reflection
Rfree0.2402 3852 1.12 %
Rwork0.2129 --
obs0.2132 344368 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.55 Å2
Refinement stepCycle: LAST / Resolution: 2.1→92.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15528 0 470 1598 17596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006816835
X-RAY DIFFRACTIONf_angle_d1.971822823
X-RAY DIFFRACTIONf_chiral_restr0.06222316
X-RAY DIFFRACTIONf_plane_restr0.0042974
X-RAY DIFFRACTIONf_dihedral_angle_d17.71056475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.40971280.352311354X-RAY DIFFRACTION92.76
2.13-2.160.411390.347612226X-RAY DIFFRACTION99.61
2.16-2.190.36471360.328312185X-RAY DIFFRACTION99.81
2.19-2.220.34841390.322612223X-RAY DIFFRACTION99.9
2.22-2.250.35441420.315112268X-RAY DIFFRACTION99.85
2.25-2.280.35941400.303912320X-RAY DIFFRACTION99.88
2.28-2.320.33421390.302712247X-RAY DIFFRACTION99.98
2.32-2.350.32791390.296412187X-RAY DIFFRACTION99.79
2.35-2.40.29231350.29412253X-RAY DIFFRACTION99.66
2.4-2.440.32311400.291412177X-RAY DIFFRACTION99.52
2.44-2.490.31981380.288512158X-RAY DIFFRACTION99.34
2.49-2.540.31521330.261512245X-RAY DIFFRACTION99.66
2.54-2.590.24851400.258412206X-RAY DIFFRACTION99.56
2.59-2.650.29941380.254712249X-RAY DIFFRACTION99.79
2.65-2.720.30851390.243812255X-RAY DIFFRACTION99.82
2.72-2.790.25621380.235212215X-RAY DIFFRACTION99.82
2.79-2.870.27071410.226712260X-RAY DIFFRACTION99.69
2.87-2.970.2691370.228212240X-RAY DIFFRACTION99.68
2.97-3.070.24461370.217612149X-RAY DIFFRACTION99.34
3.07-3.20.28121400.197112177X-RAY DIFFRACTION99.27
3.2-3.340.20641370.174512181X-RAY DIFFRACTION99.44
3.34-3.520.20591350.163712197X-RAY DIFFRACTION99.29
3.52-3.740.19921410.164812184X-RAY DIFFRACTION99.58
3.74-4.030.16981320.144912207X-RAY DIFFRACTION99.39
4.03-4.430.15341410.136112075X-RAY DIFFRACTION98.41
4.43-5.070.17891360.14312169X-RAY DIFFRACTION99.2
5.07-6.390.16571350.193612205X-RAY DIFFRACTION99.54
6.39-92.650.18351370.181411704X-RAY DIFFRACTION95.32

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