[English] 日本語
Yorodumi
- PDB-3apv: Crystal structure of the A variant of human alpha1-acid glycoprot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3apv
TitleCrystal structure of the A variant of human alpha1-acid glycoprotein and amitriptyline complex
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
ACETIC ACID / Amitriptyline / Alpha-1-acid glycoprotein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,9975
Polymers45,3832
Non-polymers6153
Water1,72996
1
A: Alpha-1-acid glycoprotein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0293
Polymers22,6911
Non-polymers3372
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)22,9692
Polymers22,6911
Non-polymers2771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.650, 45.948, 120.732
Angle α, β, γ (deg.)90.00, 92.14, 90.00
Int Tables number5
Space group name H-MC121

-
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-TP0 / Amitriptyline / 3-(10,11-dihydro-5H-dibenzo[a,d][7]annulen-5-ylidene)-N,N-dimethylpropan-1-amine


Mass: 277.403 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N / Comment: antidepressant*YM
#3: Chemical ChemComp-ACY / ACETIC ACID


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


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.57 %
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

-
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: 2.15→50 Å / Num. all: 20082 / Num. obs: 20082 / % possible obs: 98.8 % / Rmerge(I) obs: 0.059 / Rsym value: 0.524
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 8.1 / % possible all: 93.8

-
Processing

Software
NameVersionClassification
CNSrefinement
REFMAC5.5.0099refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3APU

3apu


Resolution: 2.15→36.31 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.91 / SU B: 18.509 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26712 971 4.9 %RANDOM
Rwork0.21947 ---
obs0.22183 18955 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.721 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.07 Å2
2--0.07 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.15→36.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2869 0 46 96 3011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222998
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9594058
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8365341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81624.146164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.48415506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1881520
X-RAY DIFFRACTIONr_chiral_restr0.0980.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212344
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_it0.5821.51715
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08622778
X-RAY DIFFRACTIONr_scbond_it1.63531283
X-RAY DIFFRACTIONr_scangle_it2.6824.51280
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 59 -
Rwork0.264 1314 -
obs--93.59 %
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)
12.3834-0.10320.60061.50460.89959.1306-0.1102-0.16130.0054-0.0711-0.226-0.06180.4398-0.38140.33620.14830.04330.08950.1163-0.010.483111.773-0.32714.151
22.80861.34291.86354.00781.36648.37970.0724-0.55460.10630.1709-0.2833-0.0419-0.0732-0.9620.21090.0597-0.06720.10210.317-0.07050.242810.2013.12645.817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 172
2X-RAY DIFFRACTION2B3 - 175

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more