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- PDB-5u1b: Ferritin with Gc MtrE loop2 inserted at the N-terminus -

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Basic information

Entry
Database: PDB / ID: 5u1b
TitleFerritin with Gc MtrE loop2 inserted at the N-terminus
ComponentsMtrE protein,Ferritin chimera
KeywordsOXIDOREDUCTASE / chimera / nanoparticle / 24mer cage / immunogen
Function / homology
Function and homology information


bacterial non-heme ferritin / efflux transmembrane transporter activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / plasma membrane / cytoplasm
Similarity search - Function
RND efflux system, outer membrane lipoprotein, NodT / : / Outer membrane efflux protein / Outer membrane efflux protein / Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. ...RND efflux system, outer membrane lipoprotein, NodT / : / Outer membrane efflux protein / Outer membrane efflux protein / Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Ferritin / MtrE protein
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
Helicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.81 Å
AuthorsWang, S.
CitationJournal: FEBS Open Bio / Year: 2017
Title: Structure-based design of ferritin nanoparticle immunogens displaying antigenic loops of Neisseria gonorrhoeae.
Authors: Wang, L. / Xing, D. / Le Van, A. / Jerse, A.E. / Wang, S.
History
DepositionNov 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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: MtrE protein,Ferritin chimera
B: MtrE protein,Ferritin chimera
C: MtrE protein,Ferritin chimera
D: MtrE protein,Ferritin chimera
E: MtrE protein,Ferritin chimera
F: MtrE protein,Ferritin chimera
G: MtrE protein,Ferritin chimera
H: MtrE protein,Ferritin chimera


Theoretical massNumber of molelcules
Total (without water)172,4188
Polymers172,4188
Non-polymers00
Water19811
1
A: MtrE protein,Ferritin chimera
B: MtrE protein,Ferritin chimera
C: MtrE protein,Ferritin chimera
D: MtrE protein,Ferritin chimera
E: MtrE protein,Ferritin chimera
F: MtrE protein,Ferritin chimera
G: MtrE protein,Ferritin chimera
H: MtrE protein,Ferritin chimera

A: MtrE protein,Ferritin chimera
B: MtrE protein,Ferritin chimera
C: MtrE protein,Ferritin chimera
D: MtrE protein,Ferritin chimera
E: MtrE protein,Ferritin chimera
F: MtrE protein,Ferritin chimera
G: MtrE protein,Ferritin chimera
H: MtrE protein,Ferritin chimera

A: MtrE protein,Ferritin chimera
B: MtrE protein,Ferritin chimera
C: MtrE protein,Ferritin chimera
D: MtrE protein,Ferritin chimera
E: MtrE protein,Ferritin chimera
F: MtrE protein,Ferritin chimera
G: MtrE protein,Ferritin chimera
H: MtrE protein,Ferritin chimera


Theoretical massNumber of molelcules
Total (without water)517,25524
Polymers517,25524
Non-polymers00
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_785-y+2,x-y+3,z1
crystal symmetry operation3_475-x+y-1,-x+2,z1
Buried area70010 Å2
ΔGint-411 kcal/mol
Surface area151000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.514, 124.514, 314.885
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETARGARGAA1 - 16523 - 187
21METMETARGARGBB1 - 16523 - 187
12METMETARGARGAA1 - 16523 - 187
22METMETARGARGCC1 - 16523 - 187
13METMETARGARGAA1 - 16523 - 187
23METMETARGARGDD1 - 16523 - 187
14METMETARGARGAA1 - 16523 - 187
24METMETARGARGEE1 - 16523 - 187
15METMETARGARGAA1 - 16523 - 187
25METMETARGARGFF1 - 16523 - 187
16METMETARGARGAA1 - 16523 - 187
26METMETARGARGGG1 - 16523 - 187
17ASPASPLYSLYSAA-1 - 16621 - 188
27ASPASPLYSLYSHH-1 - 16621 - 188
18METMETLYSLYSBB1 - 16623 - 188
28METMETLYSLYSCC1 - 16623 - 188
19METMETLYSLYSBB1 - 16623 - 188
29METMETLYSLYSDD1 - 16623 - 188
110METMETLYSLYSBB1 - 16623 - 188
210METMETLYSLYSEE1 - 16623 - 188
111METMETLYSLYSBB1 - 16623 - 188
211METMETLYSLYSFF1 - 16623 - 188
112METMETLYSLYSBB1 - 16623 - 188
212METMETLYSLYSGG1 - 16623 - 188
113METMETARGARGBB1 - 16523 - 187
213METMETARGARGHH1 - 16523 - 187
114METMETLYSLYSCC1 - 16623 - 188
214METMETLYSLYSDD1 - 16623 - 188
115METMETLYSLYSCC1 - 16623 - 188
215METMETLYSLYSEE1 - 16623 - 188
116METMETLYSLYSCC1 - 16623 - 188
216METMETLYSLYSFF1 - 16623 - 188
117METMETLYSLYSCC1 - 16623 - 188
217METMETLYSLYSGG1 - 16623 - 188
118METMETARGARGCC1 - 16523 - 187
218METMETARGARGHH1 - 16523 - 187
119METMETLYSLYSDD1 - 16623 - 188
219METMETLYSLYSEE1 - 16623 - 188
120METMETLYSLYSDD1 - 16623 - 188
220METMETLYSLYSFF1 - 16623 - 188
121METMETLYSLYSDD1 - 16623 - 188
221METMETLYSLYSGG1 - 16623 - 188
122METMETARGARGDD1 - 16523 - 187
222METMETARGARGHH1 - 16523 - 187
123METMETLYSLYSEE1 - 16623 - 188
223METMETLYSLYSFF1 - 16623 - 188
124METMETLYSLYSEE1 - 16623 - 188
224METMETLYSLYSGG1 - 16623 - 188
125METMETARGARGEE1 - 16523 - 187
225METMETARGARGHH1 - 16523 - 187
126METMETLYSLYSFF1 - 16623 - 188
226METMETLYSLYSGG1 - 16623 - 188
127METMETARGARGFF1 - 16523 - 187
227METMETARGARGHH1 - 16523 - 187
128METMETARGARGGG1 - 16523 - 187
228METMETARGARGHH1 - 16523 - 187

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
MtrE protein,Ferritin chimera


Mass: 21552.273 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria), (gene. exp.) Helicobacter pylori (bacteria)
Gene: mtrE, pfr, AB991_00330, ACM31_07775, AEY53_00945 / Plasmid: pET28 / Production host: Escherichia coli #1/H766 (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q51006, UniProt: O69434, bacterial non-heme ferritin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.72 Å3/Da / Density % sol: 54.85 % / Description: hexagonal plate
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: ammonium sulfate, tris

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Data collection

DiffractionMean temperature: 137 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.545
11K, H, -L20.455
ReflectionResolution: 2.8→20 Å / Num. obs: 41284 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.166 / Net I/av σ(I): 10.105 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Diffraction-ID% possible all
2.8-2.854.50.79621970.551199.9
2.85-2.94.60.7520.5971100
2.9-2.964.70.6820.6351100
2.96-3.024.70.6050.6661100
3.02-3.084.70.5250.7081100
3.08-3.154.70.4720.8161100
3.15-3.234.70.3860.8511100
3.23-3.324.70.3910.8641100
3.32-3.414.70.40.8761100
3.41-3.524.70.2850.91100
3.52-3.654.10.3730.892145.7
3.65-3.793.70.4560.898139.6
3.79-3.973.90.160.951182.2
3.97-4.174.60.1720.966199.6
4.17-4.434.80.1510.9591100
4.43-4.774.80.1060.9811100
4.77-5.244.80.1020.9811100
5.24-5.984.80.1140.9761100
5.98-7.474.80.0870.9851100
7.47-204.60.0690.9841100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.83 Å19.89 Å
Translation7.83 Å19.89 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.6.1phasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BVF
Resolution: 2.81→19.89 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 18.82 / SU ML: 0.177 / SU R Cruickshank DPI: 0.0592 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.074
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 2273 5.5 %RANDOM
Rwork0.1771 ---
obs0.1797 38919 92.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 158.02 Å2 / Biso mean: 62.184 Å2 / Biso min: 18.38 Å2
Baniso -1Baniso -2Baniso -3
1--18.25 Å20 Å20 Å2
2---18.25 Å20 Å2
3---36.5 Å2
Refinement stepCycle: final / Resolution: 2.81→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10884 0 0 11 10895
Biso mean---38.64 -
Num. residues----1332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01911126
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210416
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9315004
X-RAY DIFFRACTIONr_angle_other_deg0.969324048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.14451324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.16526.02588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.647152044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.879158
X-RAY DIFFRACTIONr_chiral_restr0.10.21620
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212640
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022628
X-RAY DIFFRACTIONr_mcbond_it5.525.4115320
X-RAY DIFFRACTIONr_mcbond_other5.55.415319
X-RAY DIFFRACTIONr_mcangle_it7.9388.1046636
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A112000.07
12B112000.07
21A112040.08
22C112040.08
31A112640.07
32D112640.07
41A113040.05
42E113040.05
51A112080.07
52F112080.07
61A112320.08
62G112320.08
71A113600.08
72H113600.08
81B111740.07
82C111740.07
91B112400.07
92D112400.07
101B112300.07
102E112300.07
111B113580.05
112F113580.05
121B112700.07
122G112700.07
131B111880.07
132H111880.07
141C112160.08
142D112160.08
151C112120.07
152E112120.07
161C112660.07
162F112660.07
171C112980.07
172G112980.07
181C111400.09
182H111400.09
191D112740.08
192E112740.08
201D113020.07
202F113020.07
211D112820.08
212G112820.08
221D112720.07
222H112720.07
231E112640.07
232F112640.07
241E113280.07
242G113280.07
251E111940.08
252H111940.08
261F112580.07
262G112580.07
271F112260.07
272H112260.07
281G112000.08
282H112000.08
LS refinement shellResolution: 2.806→2.879 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 208 -
Rwork0.214 2878 -
all-3086 -
obs--92.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.05030.0575-0.18120.1215-0.07750.9945-0.004-0.01160.0071-0.0022-0.00610.00370.00160.05620.01010.028-0.0035-0.00590.0156-0.01440.062-111.9234188.091512.262
20.17330.0177-0.04440.0632-0.07620.43860.00150.0007-0.01670.00050.0017-0.01210.022-0.0314-0.00320.03190.012-0.00250.0184-0.00270.0556-109.0572162.843915.1133
30.1868-0.12110.05030.4371-0.24940.1504-0.02730.0081-0.0151-0.0194-0.0025-0.02940.00550.0010.02980.04520.00290.00290.0197-0.00380.0331-73.8549160.9783-31.8518
40.1593-0.20910.04221.1378-0.17140.0328-0.0545-0.0052-0.00290.01610.0726-0.0005-0.0081-0.0183-0.01810.04520.00720.00030.02180.01340.0443-96.4442166.2189-20.5796
50.31170.0160.07520.9758-0.33420.1356-0.0414-0.01140.00530.02070.0245-0.0545-0.0192-0.01440.01690.0397-0.00340.01990.0318-0.00070.0192-76.9439196.063858.8502
60.40490.01750.11110.2190.00520.10950-0.0339-0.0182-0.00040.05540.006-0.0008-0.0096-0.05540.05150.00450.00440.01810.00390.0332-98.4733187.071347.825
70.53170.32080.1310.19390.07750.28050.00950.0778-0.01770.00480.0491-0.00790.02210.0176-0.05860.0163-0.00650.00230.0213-0.00270.0725-87.9684220.89431.1201
80.35120.27410.06480.32040.07830.22760.0315-0.0016-0.00540.0161-0.0279-0.00170.00110.0125-0.00360.0168-0.0163-0.00460.03340.00850.0555-92.7256217.526926.0318
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 166
2X-RAY DIFFRACTION2B1 - 166
3X-RAY DIFFRACTION3C1 - 166
4X-RAY DIFFRACTION4D1 - 166
5X-RAY DIFFRACTION5E1 - 166
6X-RAY DIFFRACTION6F1 - 166
7X-RAY DIFFRACTION7G1 - 166
8X-RAY DIFFRACTION8H-1 - 166

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