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- PDB-5da5: Crystal structure of Rhodospirillum rubrum Rru_A0973 -

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Basic information

Entry
Database: PDB / ID: 5da5
TitleCrystal structure of Rhodospirillum rubrum Rru_A0973
ComponentsRru_A0973
KeywordsOXIDOREDUCTASE / ferritin / iron / 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 / : / EncFtn-like / Helix Hairpins / Ferritin-like superfamily / Helix non-globular / Special
Similarity search - Domain/homology
: / GLYCOLIC ACID / Encapsulated ferritin-like protein
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.064 Å
AuthorsHe, D. / Vanden Hehier, 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
China Scholarships 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
DepositionAug 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _pdbx_validate_close_contact.auth_atom_id_1 / _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
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)404,445104
Polymers400,43030
Non-polymers4,01474
Water14,556808
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)134,93237
Polymers133,47710
Non-polymers1,45627
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)134,73633
Polymers133,47710
Non-polymers1,25923
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)134,77634
Polymers133,47710
Non-polymers1,29924
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.184, 120.533, 140.250
Angle α, β, γ (deg.)90.00, 95.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ...
Rru_A0973


Mass: 13347.675 Da / Num. of mol.: 30 / Fragment: UNP residues 1-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: Rru_A0973 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2RVS1
#2: Chemical...
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H4O3
#4: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 808 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.22 % / Description: 200 um x 50 um rods
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. 0.14 M calcium acetate 15 % (w/v) PEG3350
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 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7311 Å / Relative weight: 1
ReflectionResolution: 2.064→49.63 Å / Num. all: 395746 / Num. obs: 395746 / % possible obs: 99.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.123 / Rsym value: 0.147 / Net I/σ(I): 10.6
Reflection shellResolution: 2.064→2.1 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.6 / % possible all: 88.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K6C

3k6c


Resolution: 2.064→49.627 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2061 19192 4.98 %Random Selection
Rwork0.1712 ---
obs0.173 385749 97.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.064→49.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22233 0 138 808 23179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01222828
X-RAY DIFFRACTIONf_angle_d1.26431056
X-RAY DIFFRACTIONf_dihedral_angle_d13.7688412
X-RAY DIFFRACTIONf_chiral_restr0.0553470
X-RAY DIFFRACTIONf_plane_restr0.0074046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0637-2.08710.36024780.32749351X-RAY DIFFRACTION75
2.0871-2.11170.33556530.29412352X-RAY DIFFRACTION99
2.1117-2.13740.31146620.290412224X-RAY DIFFRACTION99
2.1374-2.16450.31536260.287412379X-RAY DIFFRACTION99
2.1645-2.1930.30026160.27712348X-RAY DIFFRACTION98
2.193-2.2230.32136430.283412264X-RAY DIFFRACTION98
2.223-2.25480.30686320.27812249X-RAY DIFFRACTION98
2.2548-2.28840.31546030.275912276X-RAY DIFFRACTION98
2.2884-2.32420.2846280.257912217X-RAY DIFFRACTION98
2.3242-2.36230.25886160.224312243X-RAY DIFFRACTION98
2.3623-2.4030.23186550.209912223X-RAY DIFFRACTION98
2.403-2.44670.23366180.192712209X-RAY DIFFRACTION98
2.4467-2.49380.22816780.184312112X-RAY DIFFRACTION98
2.4938-2.54470.23566240.182912320X-RAY DIFFRACTION98
2.5447-2.60.21266560.161412271X-RAY DIFFRACTION98
2.6-2.66050.20015710.165112345X-RAY DIFFRACTION98
2.6605-2.7270.23276420.167412371X-RAY DIFFRACTION99
2.727-2.80070.21935780.168312445X-RAY DIFFRACTION99
2.8007-2.88310.23176540.161612370X-RAY DIFFRACTION99
2.8831-2.97620.19456540.150312454X-RAY DIFFRACTION100
2.9762-3.08260.18897280.156312314X-RAY DIFFRACTION100
3.0826-3.2060.23146540.173912359X-RAY DIFFRACTION100
3.206-3.35180.20817350.170312393X-RAY DIFFRACTION100
3.3518-3.52850.19896850.161712354X-RAY DIFFRACTION100
3.5285-3.74950.15116360.135912381X-RAY DIFFRACTION99
3.7495-4.03890.15886510.12612416X-RAY DIFFRACTION99
4.0389-4.44510.14916220.118812433X-RAY DIFFRACTION99
4.4451-5.08780.15136570.125712294X-RAY DIFFRACTION99
5.0878-6.40790.20036700.154512319X-RAY DIFFRACTION99
6.4079-49.64180.15326670.138412271X-RAY DIFFRACTION98

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