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- PDB-6wb6: 2.05 A resolution structure of transferrin 1 from Manduca sexta -

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Basic information

Entry
Database: PDB / ID: 6wb6
Title2.05 A resolution structure of transferrin 1 from Manduca sexta
ComponentsTransferrin
KeywordsMETAL TRANSPORT / Transferrin / ferric ion binding / iron-carbonate complex / glycosylated
Function / homology
Function and homology information


: / monoatomic ion transport / extracellular space / metal ion binding
Similarity search - Function
Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
CARBONATE ION / : / Transferrin
Similarity search - Component
Biological speciesManduca sexta (tobacco hornworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsLovell, S. / Kashipathy, M.M. / Battaile, K.P. / Weber, J.J. / Gorman, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1656388 United States
CitationJournal: Protein Sci. / Year: 2021
Title: Structural insight into the novel iron-coordination and domain interactions of transferrin-1 from a model insect, Manduca sexta.
Authors: Weber, J.J. / Kashipathy, M.M. / Battaile, K.P. / Go, E. / Desaire, H. / Kanost, M.R. / Lovell, S. / Gorman, M.J.
History
DepositionMar 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transferrin
B: Transferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,46611
Polymers147,0712
Non-polymers1,3959
Water7,602422
1
A: Transferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1365
Polymers73,5361
Non-polymers6004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3306
Polymers73,5361
Non-polymers7945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.493, 139.062, 146.696
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Transferrin /


Mass: 73535.547 Da / Num. of mol.: 2 / Fragment: Full Length / Source method: isolated from a natural source / Details: larval hemolymph / Source: (natural) Manduca sexta (tobacco hornworm) / Tissue: larval hemolymph / References: UniProt: P22297
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 429 molecules

#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45 % / Mosaicity: 0.23 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 15% (w/v) PEG 20,000, 0.1 M Hepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→47.28 Å / Num. obs: 83612 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.162 / Net I/σ(I): 7.6 / Num. measured all: 544369 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.05-2.096.60.8273008445810.6972.2100
10.65-47.286.10.08141516850.99515.598.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIXdev_3755refinement
PDB_EXTRACT3.25data extraction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→40 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.02 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2719 4065 4.87 %
Rwork0.209 79455 -
obs0.212 83520 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.48 Å2 / Biso mean: 33.4218 Å2 / Biso min: 10.15 Å2
Refinement stepCycle: final / Resolution: 2.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9917 0 87 422 10426
Biso mean--37.64 30.94 -
Num. residues----1306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.070.33571590.26927312890100
2.07-2.10.31971510.264226932844100
2.1-2.130.35771600.266726702830100
2.13-2.150.32971500.26526992849100
2.15-2.180.35181380.259826922830100
2.18-2.210.35341340.264127262860100
2.21-2.250.31161490.244426822831100
2.25-2.280.33581190.234327332852100
2.28-2.320.30631340.229927272861100
2.32-2.360.28381500.222827072857100
2.36-2.40.25921200.220627202840100
2.4-2.450.30341560.226526842840100
2.45-2.50.29541440.220327422886100
2.5-2.550.27741310.217227002831100
2.55-2.610.30661420.212627082850100
2.61-2.680.26021330.210527642897100
2.68-2.750.2851280.21527092837100
2.75-2.830.29281460.215627512897100
2.83-2.920.28281510.218727222873100
2.92-3.030.31781290.218927382867100
3.03-3.150.29791240.215327542878100
3.15-3.290.26551120.211527572869100
3.29-3.470.27841270.204627742901100
3.47-3.680.24191400.193927602900100
3.68-3.970.23751450.178427652910100
3.97-4.370.21591330.164127872920100
4.37-50.20741480.168728012949100
5-6.290.23841470.199428142961100
6.29-400.27811650.21962945311099

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