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- PDB-6fak: Human afamin orthorhombic crystal form by controlled hydration -

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Basic information

Entry
Database: PDB / ID: 6fak
TitleHuman afamin orthorhombic crystal form by controlled hydration
ComponentsAfamin
KeywordsTRANSPORT PROTEIN / human plasma / wnt binding / lipid binding
Function / homology
Function and homology information


protein transport within extracellular region / vitamin E binding / vitamin transport / protein stabilization / blood microparticle / 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Chem-PG6 / TRIETHYLENE GLYCOL / Afamin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRupp, B. / Naschberger, A. / Bowler, M.W.
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
DepositionDec 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Dec 25, 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 1.3Jul 8, 2020Group: Data collection / Category: chem_comp / Item: _chem_comp.type
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_unobs_or_zero_occ_atoms / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _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_symmetry / _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_symmetry / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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.ptnr1_label_seq_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
Revision 2.1May 31, 2023Group: Database references / Structure summary
Category: chem_comp / database_2 / pdbx_related_exp_data_set
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_related_exp_data_set.metadata_reference
Revision 2.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Afamin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,69720
Polymers67,6441
Non-polymers3,05319
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint45 kcal/mol
Surface area28010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.773, 113.325, 48.796
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 67644.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: AFAM_HUMAN / Source: (gene. exp.) Homo sapiens (human) / Gene: AFM, ALB2, ALBA / Plasmid: pFastBacHBM/TOPO / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43652

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Sugars , 2 types, 3 molecules

#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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


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

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Non-polymers , 10 types, 258 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C12H26O7 / Comment: precipitant*YM
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H14O4
#10: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#11: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C12H26O6
#12: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.24 Å3/Da / Density % sol: 45.2 % / Description: Anisotropic, needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30 % PEG 1000, 270 mM CH3COONH4, 3% 6-aminohexanoic acid (ACA). 1.5 uL 5 mg/mL Stock + 1.5 uL precipitant. Streak seeding followed by micro-seeding immediately after pipetting with no pre- ...Details: 30 % PEG 1000, 270 mM CH3COONH4, 3% 6-aminohexanoic acid (ACA). 1.5 uL 5 mg/mL Stock + 1.5 uL precipitant. Streak seeding followed by micro-seeding immediately after pipetting with no pre-equilibration of the drop. Controlled hydration experiment for data collection.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 30, 2016 / Details: Be CRL
RadiationMonochromator: C110 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.9→78.85 Å / Num. obs: 48102 / % possible obs: 98.9 % / Redundancy: 3.55 % / Biso Wilson estimate: 33.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.03 / Rrim(I) all: 0.058 / Net I/σ(I): 14.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.36 % / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 2 / Num. unique obs: 2967 / CC1/2: 0.728 / Rpim(I) all: 0.547 / Rrim(I) all: 1.031 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
autoPROCdata collection
EDNAdata collection
XSCALEdata scaling
pointlessdata scaling
BALBESphasing
ARP/wARPmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VUE

2vue


Resolution: 1.9→78.85 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 8.689 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2460 5.1 %RANDOM
Rwork0.17686 ---
obs0.17905 45558 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.477 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å20 Å2
2---1.37 Å20 Å2
3---2.69 Å2
Refinement stepCycle: 1 / Resolution: 1.9→78.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4637 0 198 242 5077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195180
X-RAY DIFFRACTIONr_bond_other_d0.0020.024709
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.9546978
X-RAY DIFFRACTIONr_angle_other_deg1.0412.9811064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8985621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61525.217253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42115915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4341524
X-RAY DIFFRACTIONr_chiral_restr0.0990.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025662
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02994
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_it2.8873.2662428
X-RAY DIFFRACTIONr_mcbond_other2.8863.2622426
X-RAY DIFFRACTIONr_mcangle_it4.6158.4923064
X-RAY DIFFRACTIONr_mcangle_other4.6158.4933065
X-RAY DIFFRACTIONr_scbond_it4.2284.6262752
X-RAY DIFFRACTIONr_scbond_other4.2124.6272752
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.46411.0753914
X-RAY DIFFRACTIONr_long_range_B_refined9.54324.575798
X-RAY DIFFRACTIONr_long_range_B_other9.53124.4015777
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 171 -
Rwork0.335 3225 -
obs--95.07 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.59090.2246-0.62040.6350.17011.0041-0.06670.1226-0.0111-0.05890.04880.06890.0434-0.22590.01790.2882-0.0206-0.02590.315-0.02080.2749-47.60414.724-15.298
20.16970.21120.06690.67460.32280.1762-0.00160.04230.0378-0.1078-0.001-0.0574-0.0541-0.02350.00250.34670.0216-0.00040.24020.01080.2741-25.32635.302-13.492
30.2124-0.3907-0.01070.959-0.2420.40690.05340.04760.00150.008-0.0751-0.06690.02760.03210.02170.28410.0154-0.00220.25390.00730.2976-14.78110.548-4.225
412.2911-4.4424-6.29372.65452.71613.409-0.2197-0.249-1.33910.7352-0.1167-0.31880.37980.04290.33640.4903-0.1211-0.41760.04350.18130.8136-9.745-12.632-1.372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 154
2X-RAY DIFFRACTION1A621
3X-RAY DIFFRACTION2A155 - 390
4X-RAY DIFFRACTION2A641 - 643
5X-RAY DIFFRACTION3A391 - 562
6X-RAY DIFFRACTION3A651 - 652
7X-RAY DIFFRACTION4A563 - 586

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