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- PDB-5okl: Human afamin monoclinic crystal form -

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Basic information

Entry
Database: PDB / ID: 5okl
TitleHuman afamin monoclinic crystal form
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 / 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
PALMITOLEIC ACID / Afamin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsRupp, B. / Naschberger, A. / Bowler, M.W.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP28395-B26 Austria
CitationJournal: Structure / Year: 2017
Title: Structural Evidence for a Role of the Multi-functional Human Glycoprotein Afamin in Wnt Transport.
Authors: Naschberger, A. / Orry, A. / Lechner, S. / Bowler, M.W. / Nurizzo, D. / Novokmet, M. / Keller, M.A. / Oemer, G. / Seppi, D. / Haslbeck, M. / Pansi, K. / Dieplinger, H. / Rupp, B.
History
DepositionJul 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Structure summary / Category: audit_author / citation
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Revision 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / 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 / 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.type_symbol / _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.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: Afamin
B: Afamin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,46710
Polymers135,2882
Non-polymers2,1798
Water4,522251
1
A: Afamin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7265
Polymers67,6441
Non-polymers1,0824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Afamin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7425
Polymers67,6441
Non-polymers1,0984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.915, 112.872, 109.228
Angle α, β, γ (deg.)90.00, 93.39, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 11 - 586 / Label seq-ID: 11 - 586

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 67644.008 Da / Num. of mol.: 2 / Mutation: TEV tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AFM, ALB2, ALBA / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43652

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Sugars , 3 types, 4 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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: isolated from a natural 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
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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 , 3 types, 255 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: Cl
#6: Chemical ChemComp-PAM / PALMITOLEIC ACID / Palmitoleic acid


Mass: 254.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C16H30O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: blocky 0.1 x 0.1 x 0.1
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.5 uL PEG 1k 30%, CH3COONH4 180mM, 3% 6-aminohexanoic acid plus 1.5 uL 5 mg/ml protein stock 20mM HEPES ph7.5 150 mM NaCl, microseeding

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96598 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 8, 2016 / Details: Focussing Monochromator
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96598 Å / Relative weight: 1
ReflectionResolution: 2.08→109.04 Å / Num. obs: 66261 / % possible obs: 89.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 50.3 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.044 / Rsym value: 0.038 / Net I/σ(I): 13.59
Reflection shellResolution: 2.08→2.21 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 1.67 / CC1/2: 0.702 / % possible all: 78.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VUE

2vue


Resolution: 2.09→109.04 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 15.25 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3296 5 %RANDOM
Rwork0.199 ---
obs0.201 62919 90.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.13 Å2
Baniso -1Baniso -2Baniso -3
1-1.97 Å20 Å2-0.06 Å2
2---2.09 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.09→109.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8994 0 141 251 9386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199485
X-RAY DIFFRACTIONr_bond_other_d0.0010.028592
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.94912839
X-RAY DIFFRACTIONr_angle_other_deg0.9722.98620136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1385.0521144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34425.032465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74415.0291713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8651545
X-RAY DIFFRACTIONr_chiral_restr0.080.21419
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110405
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021862
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_it3.7618.364531
X-RAY DIFFRACTIONr_mcbond_other3.768.3594530
X-RAY DIFFRACTIONr_mcangle_it5.57815.6335671
X-RAY DIFFRACTIONr_mcangle_other5.57915.6345672
X-RAY DIFFRACTIONr_scbond_it4.7849.5514954
X-RAY DIFFRACTIONr_scbond_other4.7849.5524955
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.52217.3777165
X-RAY DIFFRACTIONr_long_range_B_refined9.69356.44310618
X-RAY DIFFRACTIONr_long_range_B_other9.68856.39510585
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 35750 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.09→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 194 -
Rwork0.355 4361 -
obs--84.43 %
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)
13.1771-0.22390.39321.6630.62220.70470.27560.5321-0.071-0.1796-0.0631-0.49070.1726-0.2933-0.21250.3801-0.0690.02560.40740.00260.151612.885641.765333.7167
20.6426-0.2991-0.29741.1910.35410.29850.08860.10010.11120.1921-0.0431-0.1822-0.0402-0.0032-0.04550.2627-0.0019-0.06950.05520.06320.10399.566861.349756.8054
30.58060.268-0.44021.0108-0.62810.5547-0.0010.013-0.0910.0557-0.0883-0.0355-0.05450.02510.08930.2805-0.034-0.09450.06070.01330.06662.001935.169267.2537
42.9449-1.44343.7732.9089-3.77496.6091-0.0945-0.072-0.2019-0.08240.0059-0.05080.0613-0.04050.08850.25040.09090.18190.04180.04230.4953-0.656711.628772.3502
52.1347-0.6905-0.10351.80570.65281.2072-0.1678-0.36080.17370.13630.2778-0.2787-0.1728-0.1057-0.11010.25490.0586-0.06550.1154-0.04460.055714.05997.900422.9365
61.30210.42070.45610.79460.27730.66790.06920.0364-0.0417-0.19870.0297-0.05960.0820.0987-0.09890.28630.0196-0.04020.05390.02150.061812.2105-12.6423-0.4212
70.5210.04790.35161.2873-0.46230.609-0.0479-0.04750.0489-0.0603-0.07970.04110.06170.06560.12760.26280.0165-0.02410.05140.03780.08686.682314.4577-11.8702
86.53792.3725-2.63041.7948-0.22745.2407-0.31830.32760.5073-0.32210.09660.4372-0.1483-0.13610.22170.23930.0298-0.11910.02670.01280.1285.311438.1116-17.4098
914.4159-11.6792-3.83989.46763.11141.0230.51390.480.548-0.3955-0.3728-0.4599-0.1337-0.1287-0.14110.2253-0.0677-0.09720.1946-0.00390.234916.7926-7.86661.6351
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 154
2X-RAY DIFFRACTION2A155 - 390
3X-RAY DIFFRACTION2A641 - 643
4X-RAY DIFFRACTION3A391 - 562
5X-RAY DIFFRACTION3A651 - 652
6X-RAY DIFFRACTION4A563 - 586
7X-RAY DIFFRACTION5B11 - 154
8X-RAY DIFFRACTION6B155 - 390
9X-RAY DIFFRACTION6B741
10X-RAY DIFFRACTION7B391 - 562
11X-RAY DIFFRACTION7B751 - 753
12X-RAY DIFFRACTION8B563 - 586
13X-RAY DIFFRACTION9B800

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