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- PDB-6rq7: Gadolinium MRI contrast compound binding in human plasma glycopro... -

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Basic information

Entry
Database: PDB / ID: 6rq7
TitleGadolinium MRI contrast compound binding in human plasma glycoprotein afamin - resurrection of highly anisotropic data
ComponentsAfamin
KeywordsTRANSPORT PROTEIN / Afamin / glycoproteins / hydrophobic ligands / conformational variability / Wnt-signalling / gadoteridol
Function / homology
Function and homology information


protein transport within extracellular region / vitamin E binding / vitamin transport / blood microparticle / protein stabilization / extracellular space / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin
Similarity search - Domain/homology
Chem-DO3 / GADOLINIUM ATOM / Afamin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsRupp, B. / Bowler, M.W. / Naschberger, A. / Juyoux, P. / vonVelsen, J.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP28395-B26 Austria
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Controlled dehydration, structural flexibility and gadolinium MRI contrast compound binding in the human plasma glycoprotein afamin.
Authors: Naschberger, A. / Juyoux, P. / von Velsen, J. / Rupp, B. / Bowler, M.W.
History
DepositionMay 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 8, 2020Group: Data collection / Category: chem_comp / Item: _chem_comp.type
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / software / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_symmetry / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Afamin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,19610
Polymers67,6441
Non-polymers2,5529
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-10 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.352, 109.734, 48.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Afamin / / Alpha-albumin / Alpha-Alb


Mass: 67644.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AFM, ALB2, ALBA / Plasmid: PFASTBACHBM/TOPO / Cell (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43652
#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.: 1 / Source method: obtained synthetically
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
#3: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Gd / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical ChemComp-DO3 / 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID


Mass: 404.459 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H32N4O7

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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: 2.05 Å3/Da / Density % sol: 40 % / Description: Crap 0.071 x 0.074 x 0.081 mm
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Stock: 5 mg/ml AFM in 20mM HEPES pH 7.5, 150mM NaCl, incubated with 10mM Gd-DO3A Drop: 200 nL AFM stock + 200 nL of precipitate in hanging drop vapor diffusion (EMBL HTX) Precipitant: 23 to ...Details: Stock: 5 mg/ml AFM in 20mM HEPES pH 7.5, 150mM NaCl, incubated with 10mM Gd-DO3A Drop: 200 nL AFM stock + 200 nL of precipitate in hanging drop vapor diffusion (EMBL HTX) Precipitant: 23 to 28% PEG4k, 0.2M NH4SO4, 0.1 M CH3COONH4, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Guesswork / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96598 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 15, 2018 / Details: BE CRL
RadiationMonochromator: C110 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96598 Å / Relative weight: 1
ReflectionResolution: 2.69→75.24 Å / Num. obs: 9591 / % possible obs: 85.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 59.1 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.18 / Rrim(I) all: 0.2 / Net I/σ(I): 5.6
Reflection shellResolution: 2.7→3.02 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 486 / CC1/2: 0.8 / Rrim(I) all: 0.68 / % possible all: 62

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
autoPROCdata collection
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OKL_B

Resolution: 2.69→75.24 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.801 / SU B: 30.777 / SU ML: 0.567 / Cross valid method: THROUGHOUT / ESU R Free: 0.719 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33544 482 5.1 %RANDOM
Rwork0.26257 ---
obs0.26629 9041 59.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.545 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0 Å2-0 Å2
2---0.67 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.69→75.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 143 0 4009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0134027
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173694
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.6535443
X-RAY DIFFRACTIONr_angle_other_deg1.0291.5788638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5995476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8423.411214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.93415729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9861520
X-RAY DIFFRACTIONr_chiral_restr0.040.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024393
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02814
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2112.0491913
X-RAY DIFFRACTIONr_mcbond_other4.20912.0491912
X-RAY DIFFRACTIONr_mcangle_it6.90222.5832383
X-RAY DIFFRACTIONr_mcangle_other6.90222.5832384
X-RAY DIFFRACTIONr_scbond_it4.31512.9132114
X-RAY DIFFRACTIONr_scbond_other4.31412.9132115
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.34823.8363060
X-RAY DIFFRACTIONr_long_range_B_refined10.5780.0954554
X-RAY DIFFRACTIONr_long_range_B_other10.56880.0884555
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.686→2.755 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 2 -
Rwork0.355 60 -
obs--5.44 %

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