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- PDB-1o9x: HUMAN SERUM ALBUMIN COMPLEXED WITH TETRADECANOIC ACID (MYRISTIC A... -

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Basic information

Entry
Database: PDB / ID: 1o9x
TitleHUMAN SERUM ALBUMIN COMPLEXED WITH TETRADECANOIC ACID (MYRISTIC ACID) AND HEMIN
ComponentsSERUM ALBUMIN
KeywordsPLASMA PROTEIN / LIPID-BINDING / FATTY ACID TRANSPORT / HEME-BINDING
Function / homology
Function and homology information


exogenous protein binding / Ciprofloxacin ADME / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / 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 / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / 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 / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / 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
PROTOPORPHYRIN IX CONTAINING FE / MYRISTIC ACID / Albumin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsZunszain, P.A. / Ghuman, J. / Komatsu, T. / Tsuchida, E. / Curry, S.
CitationJournal: Bmc Struct.Biol. / Year: 2003
Title: Crystal Structure Analysis of Human Serum Albumin Complexed with Hemin and Fatty Acid
Authors: Zunszain, P.A. / Ghuman, J. / Komatsu, T. / Tsuchida, E. / Curry, S.
History
DepositionDec 20, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Nov 20, 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)68,5588
Polymers66,5711
Non-polymers1,9877
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)80.084, 202.702, 39.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: PICHIA PASTORIS (fungus) / References: UniProt: P02768
#2: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Compound detailsSERUM ALBUMIN, REGULATES THE COLLOIDAL OSMOTIC PRESSURE OF IT BINDS TO WATER, CA++, NA+, K+, FATTY ...SERUM ALBUMIN, REGULATES THE COLLOIDAL OSMOTIC PRESSURE OF 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 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
190 mg/mlprotein1drop
220-40 %PEG33501drop
350 mMpotassium phosphate1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 15, 2002 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 3.2→27.2 Å / Num. obs: 10938 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 8.1
Reflection shellResolution: 3.2→3.4 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.1 / % possible all: 92.4
Reflection
*PLUS
Num. obs: 10825
Reflection shell
*PLUS
% possible obs: 92.4 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
CNSphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E7G

1e7g


Resolution: 3.2→27.23 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1526339.7 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / 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
Rfree0.288 567 5.2 %RANDOM
Rwork0.231 ---
obs0.231 10825 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 103.475 Å2 / ksol: 0.281234 e/Å3
Displacement parametersBiso mean: 75.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å20 Å2
2---0.01 Å20 Å2
3---1.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3.2→27.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4368 0 111 0 4479
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
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: 3.2→3.4 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.411 96 5.4 %
Rwork0.326 1698 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2HEM.PARHEM.TOP
X-RAY DIFFRACTION3MYR.PARMYR.TOP
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98

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