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- PDB-6oci: Crystal Structure of Equine Serum Albumin in Complex with Ibuprofen -

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Basic information

Entry
Database: PDB / ID: 6oci
TitleCrystal Structure of Equine Serum Albumin in Complex with Ibuprofen
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / HELICAL / THREE-DOMAIN PROTEIN / SERUM ALBUMIN
Function / homology
Function and homology information


cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / lipid binding / protein-containing complex / DNA binding ...cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / lipid binding / protein-containing complex / DNA binding / extracellular space / 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
FORMIC ACID / IBUPROFEN / SUCCINIC ACID / Albumin / Albumin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsSekula, B. / Zielinski, K. / Bujacz, A. / Bujacz, G.
CitationJournal: Chirality / Year: 2020
Title: Structural investigations of stereoselective profen binding by equine and leporine serum albumins.
Authors: Zielinski, K. / Sekula, B. / Bujacz, A. / Szymczak, I.
History
DepositionMar 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5319
Polymers65,6261
Non-polymers9058
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.580, 93.580, 141.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Serum albumin


Mass: 65625.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: F7BAY6, UniProt: P35747*PLUS
#2: Chemical ChemComp-IBP / IBUPROFEN / 2-(4-ISOBUTYLPHENYL)PROPIONIC ACID


Mass: 206.281 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18O2 / Comment: antiinflammatory, medication*YM
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 75% Tacsimate at pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.0393 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 25, 2011 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0393 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. obs: 23211 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 14.4
Reflection shellResolution: 2.54→2.64 Å / Redundancy: 6 % / Rmerge(I) obs: 1.181 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2521 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSVERSION Jan 26, 2018data reduction
XSCALEVERSION Jan 26, 2018data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZBQ

4zbq


Resolution: 2.54→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.935 / SU B: 26.569 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R: 0.54 / ESU R Free: 0.294 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24569 1132 4.9 %RANDOM
Rwork0.16971 ---
obs0.17345 22079 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.185 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20.53 Å20 Å2
2--1.06 Å2-0 Å2
3----3.45 Å2
Refinement stepCycle: 1 / Resolution: 2.54→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4568 0 63 101 4732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194745
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1711.9916407
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53925.023213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.28615850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.481520
X-RAY DIFFRACTIONr_chiral_restr0.150.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213560
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_it2.6344.272321
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.126.42900
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0114.6712424
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.13635.9587242
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.54→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 75 -
Rwork0.325 1616 -
obs--99.94 %
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)
12.02710.41770.3821.34010.27680.59360.1736-0.15790.1288-0.22190.02870.0518-0.1543-0.0857-0.20220.207-0.07590.02650.07450.0560.134540.57741.768270.3517
20.32730.16970.48581.8618-0.14170.8352-0.06360.1197-0.0581-0.33950.1116-0.1423-0.07030.2293-0.04790.1676-0.10410.02250.1866-0.0190.028249.028322.216967.1978
30.41050.4736-0.0160.6122-0.06430.9610.0144-0.02480.05690.08520.02160.0480.02320.1613-0.03610.12190.0246-0.03590.1236-0.01770.031442.566713.028588.6913
40.1129-0.11360.12470.20570.08630.680.02750.00620.0051-0.0304-0.03670.00670.0949-0.00280.00930.1392-0.0072-0.01550.1081-0.01580.061533.28173.772269.4026
50.4756-0.0294-0.35810.04870.20022.0275-0.0314-0.07410.0582-0.0882-0.02730.01560.0569-0.03520.05870.30750.0481-0.02710.0308-0.01840.016332.35393.345142.138
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 108
2X-RAY DIFFRACTION2A109 - 232
3X-RAY DIFFRACTION3A233 - 360
4X-RAY DIFFRACTION4A361 - 491
5X-RAY DIFFRACTION5A492 - 583

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