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- PDB-6suw: Crystal structure of Rhodospirillum rubrum Rru_A0973 E31A variant -

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Basic information

Entry
Database: PDB / ID: 6suw
TitleCrystal structure of Rhodospirillum rubrum Rru_A0973 E31A variant
ComponentsUncharacterized protein
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: 2.66 Å
AuthorsMarles-Wright, J. / He, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N005570/1 United Kingdom
CitationJournal: 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.
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: 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)401,76795
Polymers398,68930
Non-polymers3,07865
Water5,927329
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)134,09636
Polymers132,89610
Non-polymers1,20026
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)133,85630
Polymers132,89610
Non-polymers95920
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)133,81629
Polymers132,89610
Non-polymers91919
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.889, 120.160, 139.368
Angle α, β, γ (deg.)90.000, 95.327, 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: GLU / Beg label comp-ID: GLU / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 10 - 90 / Label seq-ID: 10 - 90

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 10 through 90)AA
22(chain 'B' and resid 10 through 90)BB
33(chain 'C' and resid 10 through 90)CC
44(chain 'D' and resid 10 through 90)DD
55(chain 'E' and resid 10 through 90)EE
66(chain 'F' and resid 10 through 90)FF
77(chain 'G' and resid 10 through 90)GG
88(chain 'H' and resid 10 through 90)HH
99(chain 'I' and resid 10 through 90)II
1010(chain 'J' and resid 10 through 90)JJ
1111(chain 'K' and resid 10 through 90)KK
1212(chain 'L' and resid 10 through 90)LL
1313(chain 'M' and resid 10 through 90)MM
1414(chain 'N' and resid 10 through 90)NN
1515(chain 'O' and resid 10 through 90)OO
1616(chain 'P' and resid 10 through 90)PP
1717(chain 'Q' and resid 10 through 90)QQ
1818(chain 'R' and resid 10 through 90)RR
1919(chain 'S' and resid 10 through 90)SS
2020(chain 'T' and resid 10 through 90)TT
2121(chain 'U' and resid 10 through 90)UU
2222(chain 'V' and resid 10 through 90)VV
2323(chain 'W' and resid 10 through 90)WW
2424(chain 'X' and resid 10 through 90)XX
2525(chain 'Y' and resid 10 through 90)YY
2626(chain 'Z' and resid 10 through 90)ZZ
2727(chain 'a' and resid 10 through 90)aAA
2828(chain 'b' and resid 10 through 90)bBA
2929(chain 'c' and resid 10 through 90)cCA
3030(chain 'd' and resid 10 through 90)dDA

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Components

#1: Protein ...
Uncharacterized protein


Mass: 13289.639 Da / Num. of mol.: 30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1) (bacteria)
Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1
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.: 35 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 15% (w/v) PEG 3350, 0.15 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: 1.737 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 10, 2015
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.737 Å / Relative weight: 1
ReflectionResolution: 2.657→49.4 Å / Num. obs: 170103 / % possible obs: 93.3 % / Redundancy: 1.8 % / Biso Wilson estimate: 39.14 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.1359 / Rpim(I) all: 0.1231 / Rrim(I) all: 0.1839 / Net I/σ(I): 5.45
Reflection shellResolution: 2.657→2.752 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.6572 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 16471 / CC1/2: 0.517 / Rpim(I) all: 0.5777 / Rrim(I) all: 0.878 / % possible all: 90.35

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DA5

5da5


Resolution: 2.66→49.4 Å / SU ML: 0.3384 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.3886
RfactorNum. reflection% reflection
Rfree0.2341 8346 4.91 %
Rwork0.1934 --
obs0.1954 170022 93.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.35 Å2
Refinement stepCycle: LAST / Resolution: 2.66→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21988 0 65 329 22382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006822466
X-RAY DIFFRACTIONf_angle_d0.732330579
X-RAY DIFFRACTIONf_chiral_restr0.03983428
X-RAY DIFFRACTIONf_plane_restr0.00493967
X-RAY DIFFRACTIONf_dihedral_angle_d13.122513545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.690.33382510.31484921X-RAY DIFFRACTION85.57
2.69-2.720.30652600.27855321X-RAY DIFFRACTION91.34
2.72-2.750.33022790.27985391X-RAY DIFFRACTION93.36
2.75-2.790.29472660.26715367X-RAY DIFFRACTION91.8
2.79-2.820.30163120.25765264X-RAY DIFFRACTION92.62
2.82-2.860.29782360.25565395X-RAY DIFFRACTION91.96
2.86-2.90.27592780.24465265X-RAY DIFFRACTION92.18
2.9-2.950.28712920.25185323X-RAY DIFFRACTION91.88
2.95-2.990.29573320.23875222X-RAY DIFFRACTION91.32
2.99-3.040.26782770.24425253X-RAY DIFFRACTION92.12
3.04-3.090.29573250.24565342X-RAY DIFFRACTION92.8
3.09-3.150.29343020.24825357X-RAY DIFFRACTION92.77
3.15-3.210.31312990.25675279X-RAY DIFFRACTION92.83
3.21-3.280.30262720.24675332X-RAY DIFFRACTION91.29
3.28-3.350.25862480.22385162X-RAY DIFFRACTION89.54
3.35-3.430.24172960.20575413X-RAY DIFFRACTION93.73
3.43-3.510.23152680.19255414X-RAY DIFFRACTION93.92
3.51-3.610.23442780.18495615X-RAY DIFFRACTION95.56
3.61-3.710.21272590.17085437X-RAY DIFFRACTION95.44
3.71-3.830.20362570.15415549X-RAY DIFFRACTION95.21
3.83-3.970.20772650.15455543X-RAY DIFFRACTION94.9
3.97-4.130.17812600.14455416X-RAY DIFFRACTION94.08
4.13-4.310.17022390.14185608X-RAY DIFFRACTION95.79
4.31-4.540.17982910.14925532X-RAY DIFFRACTION95.96
4.54-4.830.1892360.15445508X-RAY DIFFRACTION94.37
4.83-5.20.24082630.16915475X-RAY DIFFRACTION94.41
5.2-5.720.22533070.19525522X-RAY DIFFRACTION96.44
5.72-6.550.23632920.19655622X-RAY DIFFRACTION97.13
6.55-8.240.17453090.15755462X-RAY DIFFRACTION94.95
8.24-49.40.20632970.17915366X-RAY DIFFRACTION93.2

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