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- PDB-6sv1: Crystal structure of Rhodospirillum rubrum Rru_A0973 E34A variant -

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Basic information

Entry
Database: PDB / ID: 6sv1
TitleCrystal structure of Rhodospirillum rubrum Rru_A0973 E34A variant
ComponentsEncapsulated Ferritin
KeywordsOXIDOREDUCTASE / Encapsulated ferritin / ferroxidase / ferritin
Function / homology
Function and homology information


encapsulin nanocompartment / ferroxidase / ferroxidase activity / iron ion transport / intracellular iron ion homeostasis / metal ion binding
Similarity search - Function
Ferritin-like protein / : / EncFtn-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / Encapsulated ferritin-like protein
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsMarles-Wright, J. / He, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N005570/1 United Kingdom
Citation
Journal: J.Biol.Chem. / Year: 2020
Title: Dissecting the structural and functional roles of a putative metal entry site in encapsulated ferritins.
Authors: Piergentili, C. / Ross, J. / He, D. / Gallagher, K.J. / Stanley, W.A. / Adam, L. / Mackay, C.L. / Basle, A. / Waldron, K.J. / Clarke, D.J. / Marles-Wright, J.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Marles-Wright, J.
History
DepositionSep 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Encapsulated Ferritin
B: Encapsulated Ferritin
C: Encapsulated Ferritin
D: Encapsulated Ferritin
E: Encapsulated Ferritin
F: Encapsulated Ferritin
G: Encapsulated Ferritin
H: Encapsulated Ferritin
I: Encapsulated Ferritin
J: Encapsulated Ferritin
K: Encapsulated Ferritin
L: Encapsulated Ferritin
M: Encapsulated Ferritin
N: Encapsulated Ferritin
O: Encapsulated Ferritin
P: Encapsulated Ferritin
Q: Encapsulated Ferritin
R: Encapsulated Ferritin
S: Encapsulated Ferritin
T: Encapsulated Ferritin
U: Encapsulated Ferritin
V: Encapsulated Ferritin
W: Encapsulated Ferritin
X: Encapsulated Ferritin
Y: Encapsulated Ferritin
Z: Encapsulated Ferritin
a: Encapsulated Ferritin
b: Encapsulated Ferritin
c: Encapsulated Ferritin
d: Encapsulated Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)401,08678
Polymers398,68930
Non-polymers2,39748
Water11,530640
1
A: Encapsulated Ferritin
B: Encapsulated Ferritin
C: Encapsulated Ferritin
D: Encapsulated Ferritin
E: Encapsulated Ferritin
F: Encapsulated Ferritin
G: Encapsulated Ferritin
H: Encapsulated Ferritin
I: Encapsulated Ferritin
J: Encapsulated Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,77528
Polymers132,89610
Non-polymers87918
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: Encapsulated Ferritin
L: Encapsulated Ferritin
M: Encapsulated Ferritin
N: Encapsulated Ferritin
O: Encapsulated Ferritin
P: Encapsulated Ferritin
Q: Encapsulated Ferritin
R: Encapsulated Ferritin
S: Encapsulated Ferritin
T: Encapsulated Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,65525
Polymers132,89610
Non-polymers75915
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
U: Encapsulated Ferritin
V: Encapsulated Ferritin
W: Encapsulated Ferritin
X: Encapsulated Ferritin
Y: Encapsulated Ferritin
Z: Encapsulated Ferritin
a: Encapsulated Ferritin
b: Encapsulated Ferritin
c: Encapsulated Ferritin
d: Encapsulated Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,65525
Polymers132,89610
Non-polymers75915
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.794, 120.136, 139.335
Angle α, β, γ (deg.)90.000, 95.202, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
211
221
231
241
251
261
271
281
291
301

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 8 - 90 / Label seq-ID: 8 - 90

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 8 through 90)AA
22(chain 'B' and resid 8 through 90)BB
33(chain 'C' and resid 8 through 90)CC
44(chain 'D' and resid 8 through 90)DD
55(chain 'E' and resid 8 through 90)EE
66(chain 'F' and resid 8 through 90)FF
77(chain 'G' and resid 8 through 90)GG
88(chain 'H' and resid 8 through 90)HH
99(chain 'I' and resid 8 through 90)II
1010(chain 'J' and resid 8 through 90)JJ
1111(chain 'K' and resid 8 through 90)KK
1212(chain 'L' and resid 8 through 90)LL
1313(chain 'M' and resid 8 through 90)MM
1414(chain 'N' and resid 8 through 90)NN
1515(chain 'O' and resid 8 through 90)OO
1616(chain 'P' and resid 8 through 90)PP
1717(chain 'Q' and resid 8 through 90)QQ
1818(chain 'R' and resid 8 through 90)RR
1919(chain 'S' and resid 8 through 90)SS
2020(chain 'T' and resid 8 through 90)TT
2121(chain 'U' and resid 8 through 90)UU
2222(chain 'V' and resid 8 through 90)VV
2323(chain 'W' and resid 8 through 90)WW
2424(chain 'X' and resid 8 through 90)XX
2525(chain 'Y' and resid 8 through 90)YY
2626(chain 'Z' and resid 8 through 90)ZZ
2727(chain 'a' and resid 8 through 90)aAA
2828(chain 'b' and resid 8 through 90)bBA
2929(chain 'c' and resid 8 through 90)cCA
3030(chain 'd' and resid 8 through 90)dDA

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Components

#1: Protein ...
Encapsulated Ferritin


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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2RVS1
#2: Chemical...
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 15% (w/v) PEG 3350, 0.14 M Calcium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.74 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2015
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
ReflectionResolution: 2.186→48.73 Å / Num. obs: 314834 / % possible obs: 96.37 % / Redundancy: 2.9 % / Biso Wilson estimate: 33.05 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09441 / Rpim(I) all: 0.06549 / Rrim(I) all: 0.1155 / Net I/σ(I): 8.04
Reflection shellResolution: 2.186→2.265 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.6883 / Mean I/σ(I) obs: 1.43 / Num. unique obs: 30221 / CC1/2: 0.579 / Rpim(I) all: 0.4775 / Rrim(I) all: 0.8422 / % possible all: 92.66

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5da5

5da5


Resolution: 2.19→48.73 Å / SU ML: 0.2661 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.4837
RfactorNum. reflection% reflection
Rfree0.2073 15588 4.95 %
Rwork0.1712 --
obs0.173 314739 96.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.14 Å2
Refinement stepCycle: LAST / Resolution: 2.19→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22072 0 48 640 22760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012222551
X-RAY DIFFRACTIONf_angle_d0.8930699
X-RAY DIFFRACTIONf_chiral_restr0.05023445
X-RAY DIFFRACTIONf_plane_restr0.0083984
X-RAY DIFFRACTIONf_dihedral_angle_d12.201813593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.210.30494550.28899089X-RAY DIFFRACTION88.09
2.21-2.240.30855360.26319821X-RAY DIFFRACTION94.91
2.24-2.260.32225570.26429754X-RAY DIFFRACTION94.99
2.26-2.290.3045470.25699781X-RAY DIFFRACTION95.31
2.29-2.320.28394930.23189938X-RAY DIFFRACTION95.15
2.32-2.360.26665690.22159846X-RAY DIFFRACTION95.29
2.36-2.390.24795220.2159863X-RAY DIFFRACTION95.56
2.39-2.420.25675160.20649895X-RAY DIFFRACTION96.07
2.42-2.460.23545250.20059984X-RAY DIFFRACTION96.1
2.46-2.50.24445350.20249889X-RAY DIFFRACTION95.64
2.5-2.550.28214290.26599387X-RAY DIFFRACTION90.41
2.55-2.590.26444860.200210037X-RAY DIFFRACTION96.52
2.59-2.640.23815010.17819957X-RAY DIFFRACTION96.15
2.64-2.70.2255140.17979964X-RAY DIFFRACTION96.78
2.7-2.750.24094720.188810090X-RAY DIFFRACTION96.81
2.75-2.820.23545460.178110013X-RAY DIFFRACTION96.92
2.82-2.890.20985120.171210020X-RAY DIFFRACTION96.75
2.89-2.970.24534800.175510113X-RAY DIFFRACTION96.75
2.97-3.050.23195090.175410023X-RAY DIFFRACTION96.9
3.05-3.150.22284780.177210156X-RAY DIFFRACTION97.64
3.15-3.270.21974960.192210125X-RAY DIFFRACTION97.8
3.27-3.40.23875290.182810088X-RAY DIFFRACTION97.59
3.4-3.550.20845710.162810060X-RAY DIFFRACTION97.88
3.55-3.740.16614800.147910204X-RAY DIFFRACTION98.23
3.74-3.970.14965590.132210212X-RAY DIFFRACTION98.31
3.97-4.280.16645420.124110097X-RAY DIFFRACTION98.04
4.28-4.710.14856170.123110079X-RAY DIFFRACTION98.07
4.71-5.390.17615460.148410178X-RAY DIFFRACTION98.85
5.39-6.790.21485460.168210235X-RAY DIFFRACTION98.84
6.79-48.730.17195200.158210246X-RAY DIFFRACTION98.86

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