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- PDB-3apw: Crystal structure of the A variant of human alpha1-acid glycoprot... -

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Basic information

Entry
Database: PDB / ID: 3apw
TitleCrystal structure of the A variant of human alpha1-acid glycoprotein and disopyramide complex
ComponentsAlpha-1-acid glycoprotein 2Orosomucoid
KeywordsTRANSPORT PROTEIN / beta barrel / PLASMA PROTEIN
Function / homology
Function and homology information


positive regulation of interleukin-1 production / regulation of immune system process / platelet alpha granule lumen / positive regulation of interleukin-1 beta production / acute-phase response / specific granule lumen / positive regulation of tumor necrosis factor production / azurophil granule lumen / Platelet degranulation / collagen-containing extracellular matrix ...positive regulation of interleukin-1 production / regulation of immune system process / platelet alpha granule lumen / positive regulation of interleukin-1 beta production / acute-phase response / specific granule lumen / positive regulation of tumor necrosis factor production / azurophil granule lumen / Platelet degranulation / collagen-containing extracellular matrix / blood microparticle / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Alpha-1-acid glycoprotein / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Disopyramide / Alpha-1-acid glycoprotein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsNishi, K. / Ono, T. / Nakamura, T. / Fukunaga, N. / Izumi, M. / Watanabe, H. / Suenaga, A. / Maruyama, T. / Yamagata, Y. / Curry, S. / Otagiri, M.
CitationJournal: J. Biol. Chem. / Year: 2011
Title: Structural insights into differences in drug-binding selectivity between two forms of human alpha1-acid glycoprotein genetic variants, the A and F1*S forms.
Authors: Nishi, K. / Ono, T. / Nakamura, T. / Fukunaga, N. / Izumi, M. / Watanabe, H. / Suenaga, A. / Maruyama, T. / Yamagata, Y. / Curry, S. / Otagiri, M.
History
DepositionOct 21, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1-acid glycoprotein 2
B: Alpha-1-acid glycoprotein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0624
Polymers45,3832
Non-polymers6792
Water1,33374
1
A: Alpha-1-acid glycoprotein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0312
Polymers22,6911
Non-polymers3391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-1-acid glycoprotein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0312
Polymers22,6911
Non-polymers3391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.720, 45.490, 120.600
Angle α, β, γ (deg.)90.00, 91.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-1-acid glycoprotein 2 / Orosomucoid / AGP 2 / Orosomucoid-2 / OMD 2


Mass: 22691.287 Da / Num. of mol.: 2 / Mutation: C149R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGP2, ORM2 / Plasmid: pET3c / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB(DE3) / References: UniProt: P19652
#2: Chemical ChemComp-DP0 / Disopyramide / (2S)-4-(dipropan-2-ylamino)-2-phenyl-2-(pyridin-2-yl)butanamide / Disopyramide


Mass: 339.474 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N3O / Comment: medication, antiarrhythmic, channel blocker*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.05 Å3/Da / Density % sol: 39.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG 4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40.19 Å / Num. all: 18846 / Num. obs: 18846 / % possible obs: 99.6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 26.2
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.105 / Mean I/σ(I) obs: 15.2 / % possible all: 100

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Processing

Software
NameVersionClassification
CNSrefinement
REFMAC5.5.0099refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3APU

3apu


Resolution: 2.2→37.76 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.926 / SU B: 17.676 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26339 915 4.9 %RANDOM
Rwork0.22824 ---
obs0.23005 17931 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.109 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.13 Å2
2--0.26 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 50 74 3067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223075
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9654163
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0825349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.09224.048168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58815528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0711522
X-RAY DIFFRACTIONr_chiral_restr0.0980.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212392
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.631.51755
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16822846
X-RAY DIFFRACTIONr_scbond_it1.53331320
X-RAY DIFFRACTIONr_scangle_it2.5314.51317
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 66 -
Rwork0.263 1369 -
obs--100 %
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)
12.5572-0.64060.62772.04461.53988.4985-0.045-0.0636-0.04430.1038-0.2890.08860.5861-0.36070.3340.13240.00480.03840.0697-0.01550.284711.706-0.71614.465
24.2821.85835.28324.79011.88817.8310.4046-1.20160.07710.5369-0.8378-0.16240.7059-1.23790.43320.2177-0.23450.06410.6233-0.06260.06410.4342.74345.684
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 176
2X-RAY DIFFRACTION2B2 - 177

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