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- PDB-6p8k: Escherichia coli Bacterioferritin Substituted with Zinc Protoporp... -

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Basic information

Entry
Database: PDB / ID: 6p8k
TitleEscherichia coli Bacterioferritin Substituted with Zinc Protoporphyrin IX
ComponentsBacterioferritin
KeywordsMETAL BINDING PROTEIN / OXIDOREDUCTASE / bacterioferritin / zinc protoporphyrin IX / photosensitizer / ferritin
Function / homology
Function and homology information


iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity ...iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 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_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
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
Water45,5782530
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 area105120 Å2
ΔGint-406 kcal/mol
Surface area127850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.852, 207.852, 142.657
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-203-

NA

21F-202-

NA

31C-349-

HOH

41C-449-

HOH

51F-403-

HOH

61L-451-

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, 2580 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


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


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


Mass: 102.046 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2530 / 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: 3.48 Å3/Da / Density % sol: 64.63 %
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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2017
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→19.96 Å / Num. obs: 337873 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 19.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.048 / Rrim(I) all: 0.178 / Net I/σ(I): 11.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 12.6 % / Rmerge(I) obs: 3.56 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 48968 / CC1/2: 0.48 / Rpim(I) all: 1.039 / Rrim(I) all: 3.71 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Y3Q

2y3q


Resolution: 1.7→19.96 Å / SU ML: 0.2549 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 29.2534
RfactorNum. reflection% reflection
Rfree0.2175 3891 0.59 %
Rwork0.1915 --
obs0.1916 337073 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.95 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15528 0 470 2530 18528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009716887
X-RAY DIFFRACTIONf_angle_d2.006622905
X-RAY DIFFRACTIONf_chiral_restr0.05922321
X-RAY DIFFRACTIONf_plane_restr0.0052989
X-RAY DIFFRACTIONf_dihedral_angle_d16.34026498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.43071380.398123292X-RAY DIFFRACTION100
1.72-1.740.39621360.380523288X-RAY DIFFRACTION99.99
1.74-1.770.39011420.367623368X-RAY DIFFRACTION99.98
1.77-1.790.39591350.353423255X-RAY DIFFRACTION100
1.79-1.820.29891400.33523308X-RAY DIFFRACTION99.99
1.82-1.840.36751420.324323291X-RAY DIFFRACTION99.99
1.84-1.870.3511380.32123284X-RAY DIFFRACTION99.99
1.87-1.90.34381410.307923277X-RAY DIFFRACTION99.94
1.9-1.930.34411400.311523349X-RAY DIFFRACTION99.97
1.93-1.970.31761400.275923287X-RAY DIFFRACTION99.95
1.97-2.010.2691390.243423281X-RAY DIFFRACTION99.92
2.01-2.050.27031370.227223246X-RAY DIFFRACTION99.89
2.05-2.090.2391390.210623292X-RAY DIFFRACTION99.87
2.09-2.140.22831410.188623301X-RAY DIFFRACTION99.94
2.14-2.190.22571400.176623252X-RAY DIFFRACTION99.8
2.19-2.250.20521360.176223277X-RAY DIFFRACTION99.91
2.25-2.320.19851390.164723276X-RAY DIFFRACTION99.82
2.32-2.40.18041410.163123253X-RAY DIFFRACTION99.7
2.4-2.480.21651440.163723213X-RAY DIFFRACTION99.62
2.48-2.580.18841390.164823149X-RAY DIFFRACTION99.55
2.58-2.70.20221400.171923286X-RAY DIFFRACTION99.71
2.7-2.840.21541380.169223181X-RAY DIFFRACTION99.56
2.84-3.020.16921400.166123120X-RAY DIFFRACTION99.13
3.02-3.250.19771350.154323160X-RAY DIFFRACTION99.33
3.25-3.570.14921380.135523178X-RAY DIFFRACTION99.5
3.57-4.090.14971340.13123256X-RAY DIFFRACTION99.73
4.09-5.130.15391390.13323194X-RAY DIFFRACTION99.55
5.13-19.960.18031400.171122943X-RAY DIFFRACTION98.38

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