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- PDB-5l8b: Crystal structure of Rhodospirillum rubrum Rru_A0973 mutant E62A -

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Basic information

Entry
Database: PDB / ID: 5l8b
TitleCrystal structure of Rhodospirillum rubrum Rru_A0973 mutant E62A
ComponentsUncharacterized protein
KeywordsOXIDOREDUCTASE / ferritin / iron oxidation / ferroxidase
Function / homology
Function and homology information


encapsulin nanocompartment / ferroxidase / ferroxidase activity / iron ion transport / intracellular iron ion homeostasis / metal ion binding
Similarity search - Function
Helix Hairpins - #1960 / Ferritin-like protein / Helix Hairpins / Ferritin-like superfamily / Helix non-globular / Special
Similarity search - Domain/homology
Encapsulated ferritin-like protein
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsHe, D. / Hughes, S. / Vanden-Hehir, S. / Georgiev, A. / Altenbach, K. / Tarrant, E. / Mackay, C.L. / Waldron, K.J. / Clarke, D.J. / Marles-Wright, J.
Funding support China, United Kingdom, 2items
OrganizationGrant numberCountry
Chinese Scholarship Council China
Royal SocietyRG130585 United Kingdom
CitationJournal: Elife / Year: 2016
Title: Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments.
Authors: He, D. / Hughes, S. / Vanden-Hehir, S. / Georgiev, A. / Altenbach, K. / Tarrant, E.J. / Mackay, C.L. / Waldron, K.J. / Clarke, D.J. / Marles-Wright, J.
History
DepositionJun 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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.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: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
I: Uncharacterized protein
J: Uncharacterized protein
K: Uncharacterized protein
L: Uncharacterized protein
M: Uncharacterized protein
N: Uncharacterized protein
O: Uncharacterized protein
P: Uncharacterized protein
Q: Uncharacterized protein
R: Uncharacterized protein
S: Uncharacterized protein
T: Uncharacterized protein
U: Uncharacterized protein
V: Uncharacterized protein
W: Uncharacterized protein
X: Uncharacterized protein
Y: Uncharacterized protein
Z: Uncharacterized protein
a: Uncharacterized protein
b: Uncharacterized protein
c: Uncharacterized protein
d: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)399,65154
Polymers398,68930
Non-polymers96224
Water12,647702
1
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
I: Uncharacterized protein
J: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,29720
Polymers132,89610
Non-polymers40110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41660 Å2
ΔGint-274 kcal/mol
Surface area31340 Å2
MethodPISA
2
K: Uncharacterized protein
L: Uncharacterized protein
M: Uncharacterized protein
N: Uncharacterized protein
O: Uncharacterized protein
P: Uncharacterized protein
Q: Uncharacterized protein
R: Uncharacterized protein
S: Uncharacterized protein
T: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,17717
Polymers132,89610
Non-polymers2817
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41180 Å2
ΔGint-251 kcal/mol
Surface area31320 Å2
MethodPISA
3
U: Uncharacterized protein
V: Uncharacterized protein
W: Uncharacterized protein
X: Uncharacterized protein
Y: Uncharacterized protein
Z: Uncharacterized protein
a: Uncharacterized protein
b: Uncharacterized protein
c: Uncharacterized protein
d: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,17717
Polymers132,89610
Non-polymers2817
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40350 Å2
ΔGint-266 kcal/mol
Surface area31400 Å2
MethodPISA
4
U: Uncharacterized protein
V: Uncharacterized protein
W: Uncharacterized protein
X: Uncharacterized protein
Y: Uncharacterized protein
Z: Uncharacterized protein
a: Uncharacterized protein
b: Uncharacterized protein
c: Uncharacterized protein
d: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,17717
Polymers132,89610
Non-polymers2817
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41040 Å2
ΔGint-327 kcal/mol
Surface area31130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.090, 120.228, 140.358
Angle α, β, γ (deg.)90.00, 95.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ...
Uncharacterized protein


Mass: 13289.638 Da / Num. of mol.: 30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: Rru_A0973 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2RVS1
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 702 / 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: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1-2 ul protein mixed with 1 ul well solution. 15% PEG3350 + 0.13 M CaAc
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.7291 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2015
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7291 Å / Relative weight: 1
ReflectionResolution: 2.21→48.87 Å / Num. obs: 133316 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.0979 / Rsym value: 0.1064 / Net I/σ(I): 13.74
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.009 / Mean I/σ(I) obs: 1.8 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DA5

5da5


Resolution: 2.21→48.87 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.35
RfactorNum. reflection% reflection
Rfree0.2154 8081 4.98 %
Rwork0.1646 --
obs0.1671 129264 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.21→48.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21965 0 24 702 22691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01122444
X-RAY DIFFRACTIONf_angle_d1.01530550
X-RAY DIFFRACTIONf_dihedral_angle_d13.6913528
X-RAY DIFFRACTIONf_chiral_restr0.0513424
X-RAY DIFFRACTIONf_plane_restr0.0083963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2061-2.23110.36512420.31314847X-RAY DIFFRACTION93
2.2311-2.25740.43242490.35324982X-RAY DIFFRACTION98
2.2574-2.28490.32642650.26225163X-RAY DIFFRACTION100
2.2849-2.31380.27862540.21215147X-RAY DIFFRACTION100
2.3138-2.34430.24062920.19965136X-RAY DIFFRACTION100
2.3443-2.37640.25762650.19255125X-RAY DIFFRACTION100
2.3764-2.41030.26452610.19155122X-RAY DIFFRACTION100
2.4103-2.44630.26112550.19025214X-RAY DIFFRACTION100
2.4463-2.48450.24932870.18925050X-RAY DIFFRACTION100
2.4845-2.52530.27193120.18965132X-RAY DIFFRACTION100
2.5253-2.56880.24972700.1825133X-RAY DIFFRACTION100
2.5688-2.61550.24342600.17415167X-RAY DIFFRACTION100
2.6155-2.66580.24522530.17555150X-RAY DIFFRACTION100
2.6658-2.72020.22852850.18155161X-RAY DIFFRACTION100
2.7202-2.77940.24652740.17765081X-RAY DIFFRACTION100
2.7794-2.8440.21322480.16695189X-RAY DIFFRACTION100
2.844-2.91510.24022650.17055159X-RAY DIFFRACTION100
2.9151-2.9940.23582870.17345151X-RAY DIFFRACTION100
2.994-3.0820.24732570.17595177X-RAY DIFFRACTION100
3.082-3.18150.24692600.18345126X-RAY DIFFRACTION100
3.1815-3.29520.24282650.18235158X-RAY DIFFRACTION100
3.2952-3.42710.21492740.17415177X-RAY DIFFRACTION100
3.4271-3.5830.21392860.15575104X-RAY DIFFRACTION100
3.583-3.77190.16892990.1435202X-RAY DIFFRACTION100
3.7719-4.00810.17862590.13525117X-RAY DIFFRACTION100
4.0081-4.31740.16482530.12085197X-RAY DIFFRACTION100
4.3174-4.75160.16142790.12025152X-RAY DIFFRACTION100
4.7516-5.43840.19892940.14475190X-RAY DIFFRACTION100
5.4384-6.84890.21122510.16295213X-RAY DIFFRACTION100
6.8489-49.56890.17122800.14825280X-RAY DIFFRACTION99

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