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- PDB-3apu: Crystal structure of the A variant of human alpha1-acid glycoprotein -

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Basic information

Entry
Database: PDB / ID: 3apu
TitleCrystal structure of the A variant of human alpha1-acid glycoprotein
ComponentsAlpha-1-acid glycoprotein 2
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 / : ...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 / : / blood microparticle / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Alpha-1-acid glycoprotein / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Alpha-1-acid glycoprotein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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: Advisory / Data collection / Database references / Category: citation / pdbx_unobs_or_zero_occ_atoms
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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)45,7714
Polymers45,3832
Non-polymers3882
Water1,49583
1
A: Alpha-1-acid glycoprotein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8862
Polymers22,6911
Non-polymers1941
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)22,8862
Polymers22,6911
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.107, 44.862, 120.784
Angle α, β, γ (deg.)90.00, 91.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-1-acid glycoprotein 2 / 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): Origami B (DE3) / References: UniProt: P19652
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG 4000, 0.2M ammonium acetate, 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: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jun 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 21258 / Num. obs: 21258 / % possible obs: 99.9 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 56.8
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 6.7 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BX6

3bx6
PDB Unreleased entry


Resolution: 2.1→31.99 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 14.626 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23168 1038 4.9 %RANDOM
Rwork0.1996 ---
obs0.2012 20189 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.507 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å2-0.1 Å2
2--0.68 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2903 0 26 83 3012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222984
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.954035
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3575345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02224.146164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.11915498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9281520
X-RAY DIFFRACTIONr_chiral_restr0.0950.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212322
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21187
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21969
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2135
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6811.51732
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27322803
X-RAY DIFFRACTIONr_scbond_it1.7831252
X-RAY DIFFRACTIONr_scangle_it2.8664.51232
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 73 -
Rwork0.246 1464 -
obs--98.97 %
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)
12.7593-0.17190.28212.07310.59667.2819-0.0654-0.0026-0.043-0.0278-0.19610.00230.3912-0.26620.26150.14780.02780.01880.0466-0.01920.559811.9830.12113.928
23.17910.17291.13642.47582.062111.12950.0131-0.42850.14570.1418-0.2882-0.032-0.0511-0.61580.2750.0923-0.09130.0490.1729-0.04250.433410.5142.73545.925
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 175
2X-RAY DIFFRACTION2B2 - 173

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