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

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Basic information

Entry
Database: PDB / ID: 3apx
TitleCrystal structure of the A variant of human alpha1-acid glycoprotein and chlorpromazine 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 / azurophil granule lumen / positive regulation of tumor necrosis factor production / 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 / azurophil granule lumen / positive regulation of tumor necrosis factor production / 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
ACETIC ACID / Chem-Z80 / Alpha-1-acid glycoprotein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.3Oct 12, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 8, 2023Group: 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: Alpha-1-acid glycoprotein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0703
Polymers22,6911
Non-polymers3792
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.125, 63.077, 64.957
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 1 / 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-Z80 / 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine / Chlorpromazine / Chlorpromazine


Mass: 318.864 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19ClN2S / Comment: medication, antipsychotic*YM
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 1.9 Å3/Da / Density % sol: 35.32 %
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-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 9216 / Num. obs: 9216 / % possible obs: 99.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 27.6
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 8.7 / % possible all: 95.2

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0099refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3APU

3apu


Resolution: 2.2→28.88 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.894 / SU B: 16.35 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26826 494 5.4 %RANDOM
Rwork0.20238 ---
obs0.20593 8671 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.138 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 25 138 1665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221568
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.11.9632120
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5885178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38124.18686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63115273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8951511
X-RAY DIFFRACTIONr_chiral_restr0.080.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211221
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_it0.4181.5895
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81921451
X-RAY DIFFRACTIONr_scbond_it1.2253673
X-RAY DIFFRACTIONr_scangle_it2.0514.5669
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
Rfree0.324 34 -
Rwork0.204 600 -
obs--94.77 %
Refinement TLS params.Method: refined / Origin x: -7.014 Å / Origin y: -13.521 Å / Origin z: 17.587 Å
111213212223313233
T0.0301 Å20.0066 Å20.0005 Å2-0.0034 Å20.0056 Å2--0.0738 Å2
L0.418 °2-0.0198 °20.0025 °2-0.2991 °20.1976 °2--0.9836 °2
S0.0149 Å °0.0123 Å °0.0428 Å °-0.0307 Å °-0.023 Å °0.0025 Å °-0.0431 Å °-0.0387 Å °0.0081 Å °

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