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- PDB-5id7: Crystal structure of human serum albumin in complex with phosphor... -

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Basic information

Entry
Database: PDB / ID: 5id7
TitleCrystal structure of human serum albumin in complex with phosphorodithioate derivative of myristoyl cyclic phosphatidic acid (cPA)
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Helical / Three-domain protein / Serum Albumin / Drugs delivery / cyclic phosphatidic acid / lysophospholipid
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity / Aspirin ADME / 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-6A4 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsSekula, B. / Bujacz, A. / Rytczak, P. / Bujacz, G.
Funding support Poland, 3items
OrganizationGrant numberCountry
Polish Ministry of Science and Higher EducationN N405 3639 39 Poland
National Science Centre Poland2013/11/B/ST5/02271 Poland
National Science Centre Poland2014/12/T/ST5/00136 Poland
CitationJournal: Biosci.Rep. / Year: 2016
Title: Structural evidence of the species-dependent albumin binding of the modified cyclic phosphatidic acid with cytotoxic properties.
Authors: Sekula, B. / Ciesielska, A. / Rytczak, P. / Koziokiewicz, M. / Bujacz, A.
History
DepositionFeb 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,28514
Polymers133,1422
Non-polymers3,14212
Water5,585310
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2708
Polymers66,5711
Non-polymers1,6997
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0146
Polymers66,5711
Non-polymers1,4435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.895, 85.167, 96.308
Angle α, β, γ (deg.)105.46, 89.78, 101.34
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 3 - 584 / Label seq-ID: 3 - 584

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Serum albumin /


Mass: 66571.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: blood / References: UniProt: P02768
#2: Chemical
ChemComp-6A4 / (4S)-2-sulfanylidene-4-[(tetradecanoyloxy)methyl]-1,3,2lambda~5~-dioxaphospholane-2-thiolate


Mass: 395.537 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H32O4PS2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 28% PEG3350, 50 mM phosphate buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 7, 2014
RadiationMonochromator: Si (111), Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.26→46.35 Å / Num. obs: 49652 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 44.88 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.4
Reflection shellResolution: 2.26→2.4 Å / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.3 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A73

3a73


Resolution: 2.26→45.9 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / SU B: 15.61 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.487 / ESU R Free: 0.264 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25262 1012 2 %RANDOM
Rwork0.2064 ---
obs0.20734 48640 93.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.163 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.6 Å20.06 Å2
2--1.35 Å20.79 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 2.26→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9260 0 195 310 9765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0199679
X-RAY DIFFRACTIONr_bond_other_d0.0070.029275
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.91613035
X-RAY DIFFRACTIONr_angle_other_deg1.2672.97821541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37851166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14224.889450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.34151749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7341549
X-RAY DIFFRACTIONr_chiral_restr0.1170.21422
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02110615
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022054
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_it2.8543.1074658
X-RAY DIFFRACTIONr_mcbond_other2.8553.1064657
X-RAY DIFFRACTIONr_mcangle_it4.3364.6575820
X-RAY DIFFRACTIONr_mcangle_other4.3364.6575821
X-RAY DIFFRACTIONr_scbond_it3.2333.4745021
X-RAY DIFFRACTIONr_scbond_other3.2323.4745021
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0135.0617214
X-RAY DIFFRACTIONr_long_range_B_refined7.48225.01111505
X-RAY DIFFRACTIONr_long_range_B_other7.47724.97311466
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 68688 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.262→2.321 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 74 -
Rwork0.326 3147 -
obs--83.04 %
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)
11.98040.9951-0.3760.7454-0.57060.7296-0.07670.060.06450.05770.11990.0266-0.1016-0.0838-0.04320.09590.0752-0.01220.11940.01050.15521.41142.82927.511
20.63410.2749-0.87820.26830.13333.0159-0.04260.0697-0.0693-0.0335-0.0024-0.05260.0012-0.25130.04490.05520.02480.03620.17730.04280.1186-8.12622.84232.828
30.82560.17370.1370.48931.1963.0375-0.1401-0.0382-0.1294-0.157-0.04380.0479-0.3762-0.08670.18390.16460.0033-0.04590.11160.02690.058-9.89326.3427.167
40.8486-0.7464-0.28830.6640.16572.38510.07240.0339-0.0145-0.0684-0.04990.02780.09620.0669-0.02250.1406-0.03890.01850.1366-0.01540.0817-3.4518.192-7.947
51.1165-0.1647-0.05740.2567-0.45150.9183-0.0087-0.06830.0372-0.02050.025-0.00490.0302-0.0214-0.01640.0491-0.02030.00080.1439-0.00460.1556-0.4092.51920.568
60.2828-0.0935-0.36890.2027-0.42453.2437-0.10740.02240.16620.10170.016-0.10150.34630.02360.09150.24460.0331-0.0120.04960.01750.13771.65-8.39341.392
71.9063-0.94750.26970.9681-0.85081.1116-0.0493-0.0407-0.1025-0.0480.11810.07780.0853-0.0698-0.06870.0178-0.03890.00350.15160.00490.1945-17.5381.29165.605
80.3674-0.02020.64340.3070.48052.4475-0.0877-0.0260.14670.0429-0.0563-0.04580.0867-0.22520.1440.1018-0.0089-0.03730.1720.03440.1124-27.13221.33760.433
91.4547-0.1996-0.3410.65041.35172.8212-0.1883-0.0227-0.00220.1764-0.04910.10550.3562-0.07580.23750.14020.02170.04850.11440.06230.068-28.90317.61186.171
100.45070.6070.26041.1032-0.31391.81460.0693-0.01650.0120.2282-0.08790.0189-0.23590.04430.01860.20010.0442-0.02760.1717-0.00770.0569-22.8135.964101.342
110.95840.2276-0.43020.2087-0.29360.6309-0.02590.0340.04730.00380.0252-0.02230.0828-0.01450.00070.04860.0462-0.01760.1280.01170.1771-19.36641.35572.841
120.0926-0.0758-0.35340.927-0.09133.05320.0869-0.0408-0.009-0.6158-0.0581-0.2941-0.3393-0.319-0.02870.46240.08850.20730.19760.09750.1295-16.74652.31852.048
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 110
2X-RAY DIFFRACTION2A111 - 205
3X-RAY DIFFRACTION3A206 - 299
4X-RAY DIFFRACTION4A300 - 381
5X-RAY DIFFRACTION5A382 - 492
6X-RAY DIFFRACTION6A493 - 584
7X-RAY DIFFRACTION7B3 - 110
8X-RAY DIFFRACTION8B111 - 205
9X-RAY DIFFRACTION9B206 - 299
10X-RAY DIFFRACTION10B300 - 381
11X-RAY DIFFRACTION11B382 - 492
12X-RAY DIFFRACTION12B493 - 584

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