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- PDB-5l89: Crystal structure of Rhodospirillum rubrum Rru_A0973 mutant E32A -

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Basic information

Entry
Database: PDB / ID: 5l89
TitleCrystal structure of Rhodospirillum rubrum Rru_A0973 mutant E32A
ComponentsRru_A0973
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: 2.59 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. / 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 1.1Sep 7, 2016Group: Database references
Revision 1.2Jan 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.ptnr2_auth_asym_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.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.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: Rru_A0973
B: Rru_A0973
C: Rru_A0973
D: Rru_A0973
E: Rru_A0973
F: Rru_A0973
G: Rru_A0973
H: Rru_A0973
I: Rru_A0973
J: Rru_A0973
K: Rru_A0973
L: Rru_A0973
M: Rru_A0973
N: Rru_A0973
O: Rru_A0973
P: Rru_A0973
Q: Rru_A0973
R: Rru_A0973
S: Rru_A0973
T: Rru_A0973
U: Rru_A0973
V: Rru_A0973
W: Rru_A0973
X: Rru_A0973
Y: Rru_A0973
Z: Rru_A0973
a: Rru_A0973
b: Rru_A0973
c: Rru_A0973
d: Rru_A0973
hetero molecules


Theoretical massNumber of molelcules
Total (without water)399,05039
Polymers398,68930
Non-polymers3619
Water6,269348
1
A: Rru_A0973
B: Rru_A0973
C: Rru_A0973
D: Rru_A0973
E: Rru_A0973
F: Rru_A0973
G: Rru_A0973
H: Rru_A0973
I: Rru_A0973
J: Rru_A0973
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,97712
Polymers132,89610
Non-polymers802
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41480 Å2
ΔGint-241 kcal/mol
Surface area31400 Å2
MethodPISA
2
K: Rru_A0973
L: Rru_A0973
M: Rru_A0973
N: Rru_A0973
O: Rru_A0973
P: Rru_A0973
Q: Rru_A0973
R: Rru_A0973
S: Rru_A0973
T: Rru_A0973
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,05714
Polymers132,89610
Non-polymers1604
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41760 Å2
ΔGint-238 kcal/mol
Surface area30900 Å2
MethodPISA
3
U: Rru_A0973
V: Rru_A0973
W: Rru_A0973
X: Rru_A0973
Y: Rru_A0973
Z: Rru_A0973
a: Rru_A0973
b: Rru_A0973
c: Rru_A0973
d: Rru_A0973
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,01713
Polymers132,89610
Non-polymers1203
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40360 Å2
ΔGint-240 kcal/mol
Surface area31150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.783, 120.281, 140.534
Angle α, β, γ (deg.)90.00, 95.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ...
Rru_A0973


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: Plasmid / Details (production host): 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.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 40.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1-2 ul protein mixed with 1 ul well solution over 1 ml well solution 14% PEG3350 + 0.14 M CaAc
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.7311 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2015
RadiationMonochromator: Double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7311 Å / Relative weight: 1
ReflectionResolution: 2.59→48.84 Å / Num. obs: 100067 / % possible obs: 99 % / Redundancy: 4.1 % / CC1/2: 0.985 / Rmerge(I) obs: 0.171 / Rsym value: 0.196 / Net I/σ(I): 8.46
Reflection shellResolution: 2.59→2.683 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.792 / Mean I/σ(I) obs: 1.79 / % 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: 2.59→48.84 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.48
RfactorNum. reflection% reflection
Rfree0.2211 4998 5 %
Rwork0.1863 --
obs0.188 100039 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.59→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22005 0 9 348 22362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322483
X-RAY DIFFRACTIONf_angle_d0.5330603
X-RAY DIFFRACTIONf_dihedral_angle_d12.26413553
X-RAY DIFFRACTIONf_chiral_restr0.0323431
X-RAY DIFFRACTIONf_plane_restr0.0043971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5902-2.61970.32751420.29232937X-RAY DIFFRACTION92
2.6197-2.65050.3031740.27023181X-RAY DIFFRACTION99
2.6505-2.68280.35341680.2593132X-RAY DIFFRACTION100
2.6828-2.71680.35751530.2813170X-RAY DIFFRACTION99
2.7168-2.75250.33541690.28423113X-RAY DIFFRACTION99
2.7525-2.79020.30391530.26523214X-RAY DIFFRACTION99
2.7902-2.83010.32211750.25433117X-RAY DIFFRACTION99
2.8301-2.87230.29051660.23923199X-RAY DIFFRACTION99
2.8723-2.91720.27071500.24263122X-RAY DIFFRACTION99
2.9172-2.9650.33171510.24363145X-RAY DIFFRACTION99
2.965-3.01610.29261690.24333123X-RAY DIFFRACTION99
3.0161-3.0710.27951780.23183175X-RAY DIFFRACTION99
3.071-3.130.29761680.22883183X-RAY DIFFRACTION100
3.13-3.19390.26991770.24193170X-RAY DIFFRACTION100
3.1939-3.26330.26691580.24233176X-RAY DIFFRACTION100
3.2633-3.33920.24181640.21943167X-RAY DIFFRACTION100
3.3392-3.42270.23351630.18933196X-RAY DIFFRACTION100
3.4227-3.51530.21811790.17443171X-RAY DIFFRACTION100
3.5153-3.61870.20121740.16713187X-RAY DIFFRACTION100
3.6187-3.73540.1981680.15193148X-RAY DIFFRACTION100
3.7354-3.86890.17471710.14383221X-RAY DIFFRACTION100
3.8689-4.02370.1681820.14563155X-RAY DIFFRACTION100
4.0237-4.20680.17341590.13633196X-RAY DIFFRACTION100
4.2068-4.42840.14581540.13433219X-RAY DIFFRACTION100
4.4284-4.70570.17631540.13463207X-RAY DIFFRACTION100
4.7057-5.06870.1781650.15173173X-RAY DIFFRACTION100
5.0687-5.57810.21521820.16853198X-RAY DIFFRACTION100
5.5781-6.38390.21221830.1863208X-RAY DIFFRACTION100
6.3839-8.03740.19261700.16163218X-RAY DIFFRACTION100
8.0374-49.59720.17021790.1713220X-RAY DIFFRACTION98

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