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- PDB-3kq0: Crystal structure of human alpha1-acid glycoprotein -

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Basic information

Entry
Database: PDB / ID: 3kq0
TitleCrystal structure of human alpha1-acid glycoprotein
ComponentsAlpha-1-acid glycoprotein 1
KeywordsSIGNALING PROTEIN / PLASMA PROTEIN / GLYCOPROTEIN / POLYMORPHISM / ACUTE PHASE PROTEIN / SECRETED / PYRROLIDONE CARBOXYLIC ACID / LIPOCALIN
Function / homology
Function and homology information


positive regulation of tumor necrosis factor production => GO:0032760 / neutrophil degranulation / platelet degranulation / positive regulation of interleukin-1 production / regulation of immune system process / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / platelet alpha granule lumen / positive regulation of interleukin-1 beta production / acute-phase response ...positive regulation of tumor necrosis factor production => GO:0032760 / neutrophil degranulation / platelet degranulation / positive regulation of interleukin-1 production / regulation of immune system process / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / platelet alpha granule lumen / positive regulation of interleukin-1 beta production / acute-phase response / specific granule lumen / tertiary granule lumen / Platelet degranulation / collagen-containing extracellular matrix / blood microparticle / inflammatory response / 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
(2R)-2,3-dihydroxypropyl acetate / Alpha-1-acid glycoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / UV-RIP / Resolution: 1.8 Å
AuthorsSchiefner, A. / Schonfeld, D.L. / Ravelli, R.B.G. / Mueller, U. / Skerra, A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The 1.8-A crystal structure of alpha1-acid glycoprotein (Orosomucoid) solved by UV RIP reveals the broad drug-binding activity of this human plasma lipocalin.
Authors: Schonfeld, D.L. / Ravelli, R.B. / Mueller, U. / Skerra, A.
History
DepositionNov 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
SupersessionFeb 9, 2010ID: 3BX6
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,8513
Polymers22,6811
Non-polymers1702
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.894, 78.894, 93.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 22681.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGP-A, AGP1, ORM, ORM1 / Plasmid: pAGP1 / Production host: Escherichia coli (E. coli) / Strain (production host): MC4100(DELTA)SKP / References: UniProt: P02763
#2: Chemical ChemComp-JIM / (2R)-2,3-dihydroxypropyl acetate / (1R)-1-glycerol acetate


Mass: 134.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE LIGAND JIM HAS BEEN MODELLED ACCORDING TO THE FOBS BUT WAS NOT VERIFIED BY BIOCHEMICAL METHODS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
13.261.6The structure factor file contains both the native Fobs and the Fobs with UV-radiation damage (crystal condition no 2).
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop6.41.9 M SODIUM/POTASSIUM PHOSPHATE, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop6.92.2 M SODIUM/POTASSIUM PHOSPHATE, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-111.0054
SYNCHROTRONBESSY 14.120.9184
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 13, 2006
MARMOSAIC 225 mm CCD2CCDMar 9, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single crystalSINGLE WAVELENGTHMx-ray1
2Double crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.00541
20.91841
ReflectionResolution: 1.8→20 Å / Num. obs: 26679 / % possible obs: 97.7 % / Redundancy: 9.5 % / Rsym value: 0.059 / Net I/σ(I): 31.5
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.406 / % possible all: 82.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: UV-RIP / Resolution: 1.8→19.72 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.222 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23963 1374 5 %RANDOM
Rwork0.20178 ---
obs0.20364 25898 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2---0.77 Å20 Å2
3---1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1454 0 10 142 1606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0221500
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1571.9532036
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7025174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.8182580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10315257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.74157
X-RAY DIFFRACTIONr_chiral_restr0.1810.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211154
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_it1.6111.5876
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.77121429
X-RAY DIFFRACTIONr_scbond_it3.933624
X-RAY DIFFRACTIONr_scangle_it6.2164.5607
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 84 -
Rwork0.32 1519 -
obs--80.96 %

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