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- PDB-1gnj: HUMAN SERUM ALBUMIN COMPLEXED WITH cis-5,8,11,14-EICOSATETRAENOIC... -

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Basic information

Entry
Database: PDB / ID: 1gnj
TitleHUMAN SERUM ALBUMIN COMPLEXED WITH cis-5,8,11,14-EICOSATETRAENOIC ACID (ARACHIDONIC ACID)
ComponentsSERUM ALBUMIN
KeywordsPLASMA PROTEIN / METAL-BINDING / LIPID-BINDING / GLYCOPROTEIN
Function / homology
Function and homology information


Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / platelet alpha granule lumen / fatty acid binding / cellular response to starvation / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / endoplasmic reticulum lumen / copper ion binding / endoplasmic reticulum / Golgi apparatus / protein-containing complex / extracellular space / DNA binding / extracellular exosome / extracellular region / identical protein binding / nucleus / 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
ARACHIDONIC ACID / Albumin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPetitpas, I. / Gruene, T. / Bhattacharya, A.A. / Curry, S.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal Structures of Human Serum Albumin Complexed with Monounsaturated and Polyunsaturated Fatty Acids.
Authors: Petitpas, I. / Gruene, T. / Bhattacharya, A.A. / Curry, S.
History
DepositionOct 5, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERUM ALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0079
Polymers66,5711
Non-polymers2,4368
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)190.219, 38.972, 96.236
Angle α, β, γ (deg.)90.00, 105.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SERUM ALBUMIN


Mass: 66571.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P02768
#2: Chemical
ChemComp-ACD / ARACHIDONIC ACID


Mass: 304.467 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION:SERUM ALBUMIN, REGULATES THE COLLOIDAL OSMOTIC PRESSURE PRESSURE OF BLOOD. IT BINDS TO ...FUNCTION:SERUM ALBUMIN, REGULATES THE COLLOIDAL OSMOTIC PRESSURE PRESSURE OF BLOOD. IT BINDS TO WATER, CA++, NA+, K+, FATTY ACIDS HORMONES, BILIRUBIN AND DRUGS
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: 2.66 Å3/Da / Density % sol: 54 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mg/mlprotein1drop
236-37 %(w/v)PEG33501reservoir
350 mMpotassium phosphate1reservoirpH7.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9102
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2000 / Details: MIRRORS
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9102 Å / Relative weight: 1
ReflectionResolution: 2.6→29.6 Å / Num. obs: 20374 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 57.8 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 5.4
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.3 / % possible all: 76
Reflection shell
*PLUS
% possible obs: 76 %

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BJ5

1bj5


Resolution: 2.6→29.62 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1638392.64 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED RESIDUES ASP 1, ALA 2 AND LEU 585 ARE DISORDERED AND HAVE NOT BEEN INCLUDED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 971 4.8 %RANDOM
Rwork0.194 ---
obs0.194 20374 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.4052 Å2 / ksol: 0.285785 e/Å3
Displacement parametersBiso mean: 62.3 Å2
Baniso -1Baniso -2Baniso -3
1-11.94 Å20 Å26.62 Å2
2---0.78 Å20 Å2
3----11.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4520 0 150 9 4679
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 121 4.5 %
Rwork0.314 2542 -
obs--76 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ACD.PARACD.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shell
*PLUS
Rfactor obs: 0.314

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