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- PDB-2hzq: Crystal structure of human apolipoprotein D (ApoD) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2hzq
TitleCrystal structure of human apolipoprotein D (ApoD) in complex with progesterone
ComponentsApolipoprotein D
KeywordsTRANSPORT PROTEIN / lipocalin / beta barrel / bilin-binding protein
Function / homology
Function and homology information


negative regulation of lipoprotein lipid oxidation / Transport of fatty acids / negative regulation of T cell migration / negative regulation of smooth muscle cell-matrix adhesion / peripheral nervous system axon regeneration / lipid carrier activity / negative regulation of focal adhesion assembly / tissue regeneration / negative regulation of monocyte chemotactic protein-1 production / negative regulation of protein import into nucleus ...negative regulation of lipoprotein lipid oxidation / Transport of fatty acids / negative regulation of T cell migration / negative regulation of smooth muscle cell-matrix adhesion / peripheral nervous system axon regeneration / lipid carrier activity / negative regulation of focal adhesion assembly / tissue regeneration / negative regulation of monocyte chemotactic protein-1 production / negative regulation of protein import into nucleus / cholesterol binding / negative regulation of platelet-derived growth factor receptor signaling pathway / response to axon injury / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of cytokine production involved in inflammatory response / cytosolic ribosome / response to reactive oxygen species / lipid metabolic process / negative regulation of smooth muscle cell proliferation / brain development / glucose metabolic process / angiogenesis / neuronal cell body / dendrite / perinuclear region of cytoplasm / : / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Apolipoprotein D / Apolipoprotein D, vertebrates / Lipocalin-like domain / Lipocalin, ApoD type / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin ...Apolipoprotein D / Apolipoprotein D, vertebrates / Lipocalin-like domain / Lipocalin, ApoD type / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PROGESTERONE / Apolipoprotein D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsEichinger, A. / Skerra, A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural insight into the dual ligand specificity and mode of high density lipoprotein association of apolipoprotein d.
Authors: Eichinger, A. / Nasreen, A. / Kim, H.J. / Skerra, A.
History
DepositionAug 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / refine
Item: _refine.pdbx_starting_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3032
Polymers19,9881
Non-polymers3141
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.206, 49.206, 144.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Apolipoprotein D / Apo-D / ApoD


Mass: 19988.102 Da / Num. of mol.: 1 / Mutation: L23P, W99H, C116S, I118S, L120S, P133V, N134A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOD / Plasmid: pApoD27delta(QA) / Production host: Escherichia coli (E. coli) / Strain (production host): KS272 / References: UniProt: P05090
#2: Chemical ChemComp-STR / PROGESTERONE


Mass: 314.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.16 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.1 M lithium sulfate, 0.1 M ammonium formate, 0.075 M Hepes/NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0089 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 13, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0089 Å / Relative weight: 1
ReflectionResolution: 1.8→46.575 Å / Num. all: 17254 / Num. obs: 17084 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 11.3 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.911.20.3082.32643123500.30895.3
1.9-2.0111.10.2153.52490522360.21597.5
2.01-2.1510.90.1365.32385621880.13698.9
2.15-2.32110.1066.42257420530.10699.2
2.32-2.5511.20.0937.42110318910.093100
2.55-2.8511.50.0837.21986617300.083100
2.85-3.2911.40.0649.21788515720.064100
3.29-4.0211.30.04910.71503713320.049100
4.02-5.6913.20.04611.81418110730.046100
5.69-49.2111.50.0498.175626590.04999.3

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Phasing

Phasing MR
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
EPMRphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
REFMAC5.2.0003phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.714 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 860 5.1 %RANDOM
Rwork0.187 ---
all0.189 17254 --
obs0.189 17013 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.551 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--0.79 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1327 0 23 235 1585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221379
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.9611888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5265163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.3125.55663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2815224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.649154
X-RAY DIFFRACTIONr_chiral_restr0.1040.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021045
X-RAY DIFFRACTIONr_nbd_refined0.210.2590
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2951
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2176
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.212
X-RAY DIFFRACTIONr_mcbond_it1.1071.5857
X-RAY DIFFRACTIONr_mcangle_it1.73821358
X-RAY DIFFRACTIONr_scbond_it2.7943600
X-RAY DIFFRACTIONr_scangle_it4.2654.5530
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 89 -
Rwork0.211 1074 -
obs-1163 94.4 %

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