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- PDB-3cx9: Crystal Structure of Human serum albumin complexed with Myristic ... -

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Basic information

Entry
Database: PDB / ID: 3cx9
TitleCrystal Structure of Human serum albumin complexed with Myristic acid and lysophosphatidylethanolamine
ComponentsSerum albumin
KeywordsSTRUCTURAL PROTEIN / Human serum albumin / Lysophospholipids / Lysophosphatidylethanolamine / Fluorescence quenching / Cleavage on pair of basic residues / Disease mutation / Glycation / Glycoprotein / Lipid-binding / Metal-binding / Secreted
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / 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
Chem-LPX / MYRISTIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGuo, S. / Yang, F. / Chen, L. / Bian, C. / Huang, M.
CitationJournal: Biochem.J. / Year: 2009
Title: Structural basis of transport of lysophospholipids by human serum albumin.
Authors: Guo, S. / Shi, X. / Yang, F. / Chen, L. / Meehan, E.J. / Bian, C. / Huang, M.
History
DepositionApr 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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

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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)67,8677
Polymers66,2721
Non-polymers1,5956
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)183.888, 39.015, 95.633
Angle α, β, γ (deg.)90.00, 104.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serum albumin /


Mass: 66271.898 Da / Num. of mol.: 1 / Fragment: UNP residues 27-608 / Source method: isolated from a natural source / Details: human serum albumin / Source: (natural) Homo sapiens (human) / References: UniProt: P02768
#2: Chemical
ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-LPX / (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate


Mass: 453.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44NO7P

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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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 35% PEG 3350, 85mM potassium phosphate, 5mM sodium azide, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: BRUKER SMART 2000 / Detector: CCD / Date: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 15244 / % possible obs: 79.1 % / Redundancy: 2 % / Rmerge(I) obs: 0.057
Reflection shellResolution: 2.8→2.873 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.356 / Num. unique all: 1095 / % possible all: 85.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PROTEUM PLUSPLUSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N5U

1n5u


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.866 / SU B: 41.451 / SU ML: 0.366 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.469 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29527 813 5.1 %RANDOM
Rwork0.21949 ---
obs0.2234 15244 95.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.231 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20.58 Å2
2--2.15 Å20 Å2
3----3.49 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4493 0 98 0 4591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224691
X-RAY DIFFRACTIONr_bond_other_d0.0020.023335
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.986333
X-RAY DIFFRACTIONr_angle_other_deg1.0493.0088049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3925581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72524.585205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.42915779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1191523
X-RAY DIFFRACTIONr_chiral_restr0.1310.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025149
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02909
X-RAY DIFFRACTIONr_nbd_refined0.2410.21251
X-RAY DIFFRACTIONr_nbd_other0.2010.23351
X-RAY DIFFRACTIONr_nbtor_refined0.1930.22260
X-RAY DIFFRACTIONr_nbtor_other0.0920.22546
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.220
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_it0.5241.53189
X-RAY DIFFRACTIONr_mcbond_other0.0911.51155
X-RAY DIFFRACTIONr_mcangle_it0.82324682
X-RAY DIFFRACTIONr_scbond_it1.431897
X-RAY DIFFRACTIONr_scangle_it2.1744.51651
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 56 -
Rwork0.32 1131 -
obs--99.58 %
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)
14.4383-0.46380.16897.9638-0.36272.1980.0581-0.0927-0.50550.2380.0370.37320.5307-0.4771-0.0951-0.1793-0.0634-0.0260.0019-0.0052-0.1713-53.126-4.452-24.365
22.38711.3497-0.81993.308-1.99439.99080.13280.05630.1414-0.4338-0.1531-0.6339-0.36310.65210.0203-0.160.07020.1317-0.05220.0351-0.0123-33.6884.896-33.749
34.5923-1.09212.34281.2138-0.41123.85960.18210.048-0.0206-0.1463-0.1460.4429-0.3236-0.1573-0.0361-0.1285-0.02760.0332-0.0031-0.0595-0.1699-34.754.717-6.539
43.59020.0185-0.31922.7933-0.92886.18260.0285-0.74680.01070.3008-0.1018-0.4408-0.27910.66240.0733-0.2314-0.1628-0.05350.2431-0.0564-0.1855-16.0662.2186.892
54.1598-1.7288-2.62194.50452.82668.70360.13880.1224-0.0844-0.1087-0.20240.3118-0.3507-0.19280.0637-0.173-0.07140.01010.0923-0.0688-0.1588-10.474-2.312-20.615
68.3551-0.4264-0.12612.3091-0.12936.95410.22251.21390.4439-0.4785-0.11-0.1129-0.54180.5781-0.11250.0690.0051-0.00610.6018-0.0641-0.11270.612-5.457-41.385
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 106
2X-RAY DIFFRACTION1A1002
3X-RAY DIFFRACTION2A107 - 197
4X-RAY DIFFRACTION3A198 - 292
5X-RAY DIFFRACTION4A293 - 385
6X-RAY DIFFRACTION4A1006
7X-RAY DIFFRACTION5A386 - 492
8X-RAY DIFFRACTION5A1003 - 1004
9X-RAY DIFFRACTION6A493 - 584
10X-RAY DIFFRACTION6A1005

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