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- PDB-6ock: Crystal Structure of Leporine Serum Albumin in Complex with Ketoprofen -

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Basic information

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


exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / oxygen binding / pyridoxal phosphate binding / protein-folding chaperone binding ...exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / oxygen binding / pyridoxal phosphate binding / protein-folding chaperone binding / blood microparticle / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular exosome / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Chem-2J3 / (2S)-2-[3-(benzenecarbonyl)phenyl]propanoic acid / ACETATE ION / TRIETHYLENE GLYCOL / Chem-POG / Albumin / Albumin
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZielinski, K. / Sekula, B. / 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 ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 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)67,93712
Polymers66,1741
Non-polymers1,76311
Water6,593366
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)73.690, 79.480, 103.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serum albumin


Mass: 66173.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Blood / References: UniProt: G1U9S2, UniProt: P49065*PLUS

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Non-polymers , 6 types, 377 molecules

#2: Chemical ChemComp-9KL / (2S)-2-[3-(benzenecarbonyl)phenyl]propanoic acid / Dexketoprofen


Mass: 254.281 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14O3 / Comment: antiinflammatory*YM
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-POG / (20S)-2,5,8,11,14,17-HEXAMETHYL-3,6,9,12,15,18-HEXAOXAHENICOSANE-1,20-DIOL / POLYPROPYLENE GLYCOL / HEPTAPROPYLENE GLYCOL


Mass: 424.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44O8
#6: Chemical ChemComp-2J3 / (2R)-2-{[(2R)-2-{[(2R)-2-hydroxypropyl]oxy}propyl]oxy}propan-1-ol


Mass: 192.253 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C9H20O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8% PPG 400, 0.2 M ammonium acetate, 16% PEG 3350, 0.1M TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2012 / Details: MIRRORS
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 48629 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Net I/σ(I): 26.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 6810 / CC1/2: 0.677 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEVERSION Nov 1, 2016data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F5V

4f5v


Resolution: 1.9→30.08 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.424 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25263 1401 2.9 %RANDOM
Rwork0.18996 ---
obs0.19172 47209 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.529 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0 Å2
2--0.79 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4618 0 112 366 5096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194930
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0141.9886679
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0735609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46624.867226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.36315877
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9451522
X-RAY DIFFRACTIONr_chiral_restr0.1420.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213708
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_it2.2543.5292360
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.4485.2732949
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8323.8672570
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.17130.7727990
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 100 -
Rwork0.323 3406 -
obs--99.72 %
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)
11.73811.80840.0462.7532-0.47451.74390.1811-0.41440.35680.2904-0.31470.4152-0.2068-0.38430.13360.0824-0.00390.02580.1911-0.10640.092838.802119.87786.6526
22.2659-0.50021.99050.62340.11032.4332-0.2289-0.01650.14-0.01620.2092-0.1818-0.44410.17870.01970.2738-0.0172-0.07070.0669-0.05530.118657.487929.907182.9821
31.7081-0.03871.98521.3490.97653.6004-0.07730.35490.0509-0.00180.2404-0.2892-0.17330.6202-0.16310.0547-0.037-0.00080.1316-0.02760.122162.57622.4876.3498
40.97430.41470.91380.23370.33241.37380.07390.1332-0.21030.02520.1164-0.04140.01610.142-0.19020.07250.0006-0.01960.08850.00020.116347.01228.128464.0679
53.1750.1670.27330.59151.04662.60140.1610.1472-0.23740.23360.1454-0.11940.39090.2874-0.30640.0990.053-0.06480.0559-0.00910.113957.61253.352272.8807
61.9223-0.36380.24870.184-0.5712.51140.38130.0423-0.3949-0.1076-0.02250.12510.2730.3312-0.35880.13750.0645-0.09740.1575-0.16720.264248.2793-2.079747.6713
71.48270.4781.18670.15680.42854.00190.0070.3545-0.0191-0.00960.11270.0012-0.31420.4132-0.11970.0537-0.0070.01430.1755-0.10240.110546.91887.478144.0997
84.97374.90952.63017.03082.72411.3989-0.20670.6338-0.1739-0.16710.3199-0.3096-0.11040.3189-0.11320.0906-0.07280.07320.2402-0.07420.083857.497117.626642.04
94.5694-1.27170.28551.0018-0.19310.99480.05460.2058-0.1010.06150.0483-0.1079-0.169-0.0167-0.10290.06830.01950.02260.0344-0.01680.063756.856638.045853.2129
101.5686-0.2741-0.19471.08430.08590.46690.01980.0037-0.1690.06140.1031-0.1041-0.137-0.01-0.12290.0884-0.01510.01610.03210.00460.087155.301127.524858.0869
111.14150.50280.60454.2371-0.3781.1903-0.04480.19220.005-0.25150.08160.03210.0729-0.1764-0.03680.0724-0.01410.00530.13930.02340.036244.189530.443149.6243
121.8776-1.42580.31451.14780.27375.0649-0.1177-0.31350.44070.07010.2736-0.3286-0.6520.1965-0.15590.2054-0.00890.08950.0648-0.0840.189755.352349.350562.1064
130.89031.05861.7553.29874.14395.604-0.234-0.23160.34180.0022-0.10380.0712-0.2538-0.14680.33780.3298-0.0325-0.0160.2865-0.04480.335261.332256.973159.3275
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 106
2X-RAY DIFFRACTION2A107 - 147
3X-RAY DIFFRACTION3A148 - 198
4X-RAY DIFFRACTION4A199 - 250
5X-RAY DIFFRACTION5A251 - 295
6X-RAY DIFFRACTION6A296 - 336
7X-RAY DIFFRACTION7A337 - 366
8X-RAY DIFFRACTION8A367 - 398
9X-RAY DIFFRACTION9A399 - 417
10X-RAY DIFFRACTION10A418 - 468
11X-RAY DIFFRACTION11A469 - 497
12X-RAY DIFFRACTION12A498 - 537
13X-RAY DIFFRACTION13A538 - 584

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