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- PDB-6hn1: Complex of Caprine Serum Albumin with diclofenac -

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Basic information

Entry
Database: PDB / ID: 6hn1
TitleComplex of Caprine Serum Albumin with diclofenac
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / Caprine serum albumin / Goat serum albumin / diclofenac / nonsteroidal anti-inflammatory drugs
Function / homology
Function and homology information


blood microparticle / lipid binding / metal ion binding / cytoplasm
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin ...Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID / Albumin / Albumin
Similarity search - Component
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsTalaj, J.A. / Bujacz, A. / Bujacz, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
2013/11/B/ST5/02271 Poland
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Investigation of Diclofenac Binding to Ovine, Caprine, and Leporine Serum Albumins.
Authors: Talaj, J.A. / Zielinski, K. / Bujacz, A.
History
DepositionSep 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2258
Polymers66,4131
Non-polymers1,8127
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-54 kcal/mol
Surface area26970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.960, 66.280, 212.580
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 Albumin


Mass: 66412.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / References: UniProt: B3VHM9, UniProt: A0A452F7K4*PLUS
#2: Chemical
ChemComp-DIF / 2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID / DICLOFENAC


Mass: 296.149 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H11Cl2NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory, medication*YM
#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.: 501 / 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: 2.24 Å3/Da / Density % sol: 45.11 % / Description: rhomboid prism
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Jeffamine ED2001, citric buffer pH 5.0, BaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 24, 2014
RadiationMonochromator: Si 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 85408 / % possible obs: 97.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 28.027 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.13
Reflection shellResolution: 1.55→1.65 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 13473 / CC1/2: 0.669 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ORI

5ori


Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.833 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.094 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23853 1111 1.3 %RANDOM
Rwork0.16481 ---
obs0.16579 84295 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.027 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å2-0 Å2-0 Å2
2---0.54 Å2-0 Å2
3---1.23 Å2
Refinement stepCycle: 1 / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4643 0 115 501 5259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0194960
X-RAY DIFFRACTIONr_bond_other_d0.0060.024643
X-RAY DIFFRACTIONr_angle_refined_deg1.9811.9266725
X-RAY DIFFRACTIONr_angle_other_deg1.1782.98810800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0275608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40124.956228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67415901
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1151524
X-RAY DIFFRACTIONr_chiral_restr0.1360.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215550
X-RAY DIFFRACTIONr_gen_planes_other0.0190.021090
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_it4.1692.5012357
X-RAY DIFFRACTIONr_mcbond_other4.1682.52356
X-RAY DIFFRACTIONr_mcangle_it5.0713.7562951
X-RAY DIFFRACTIONr_mcangle_other5.0713.7572952
X-RAY DIFFRACTIONr_scbond_it5.442.9682603
X-RAY DIFFRACTIONr_scbond_other5.4392.9682604
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2174.293762
X-RAY DIFFRACTIONr_long_range_B_refined6.57621.7376310
X-RAY DIFFRACTIONr_long_range_B_other6.46121.4166087
X-RAY DIFFRACTIONr_rigid_bond_restr3.59839603
X-RAY DIFFRACTIONr_sphericity_free29.7325136
X-RAY DIFFRACTIONr_sphericity_bonded15.92959837
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 70 -
Rwork0.256 5650 -
obs--90.82 %

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