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- PDB-8ey5: Human Serum Albumin with Cobalt (II) and Myristic Acid - crystal 3 -

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Basic information

Entry
Database: PDB / ID: 8ey5
TitleHuman Serum Albumin with Cobalt (II) and Myristic Acid - crystal 3
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / serum albumin / complex with cobalt / albumin with fatty acid / Structural Genomics / PSI-Biology / Center for Structural Genomics of Infectious Diseases / CSGID / Center for Structural Biology of Infectious Diseases / CSBID
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 / cellular response to starvation / 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
: / MYRISTIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGucwa, M. / Cooper, D.R. / Stewart, A.J. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM132595 United States
CitationJournal: Chem Sci / Year: 2023
Title: Structural and biochemical characterisation of Co2+-binding sites on serum albumins and their interplay with fatty acids
Authors: Wu, D. / Gucwa, M. / Czub, M.P. / Cooper, D.R. / Shabalin, I.G. / Fritzen, R. / Arya, S. / Schwarz-Linek, U. / Blindauer, C.A. / Minor, W. / Stewart, A.J.
History
DepositionOct 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Other / Structure summary / Category: audit_author / pdbx_SG_project / struct_keywords / Item: _struct_keywords.text
Revision 2.0Mar 22, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / pdbx_contact_author / pdbx_database_related / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_planes / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns_shell / software / struct_conf / struct_conn / struct_mon_prot_cis
Item: _entity.pdbx_number_of_molecules / _pdbx_struct_assembly_prop.value ..._entity.pdbx_number_of_molecules / _pdbx_struct_assembly_prop.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R_Free / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _software.classification / _software.name / _software.version / _struct_mon_prot_cis.pdbx_omega_angle
Description: Polymer geometry
Details: Improved clashscore, ramachandran outliers, sidechain outliers. Improved water molecule ligands in metal sites.
Provider: author / Type: Coordinate replacement
Revision 2.1Apr 19, 2023Group: Author supporting evidence / Category: pdbx_audit_support
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.4Oct 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)68,92115
Polymers66,5711
Non-polymers2,35014
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint9 kcal/mol
Surface area28140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.966, 38.548, 93.409
Angle α, β, γ (deg.)90.000, 103.750, 90.000
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 natural source / Source: (natural) Homo sapiens (human) / Tissue: Blood / References: UniProt: P02768
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.45 Å3/Da / Density % sol: 49 % / Description: Rectangular prisms
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 200 nL 22.5% PEG Smear Low, 10% isopropanol, 100 mM Tris, pH 7.4 + 200 nL 88 mg/mL albumin, saturated with myristic acid, 50 mM sodium chloride, 25 mM Tris, pH 7.4. 400 nL 45% PEG Smear Low, ...Details: 200 nL 22.5% PEG Smear Low, 10% isopropanol, 100 mM Tris, pH 7.4 + 200 nL 88 mg/mL albumin, saturated with myristic acid, 50 mM sodium chloride, 25 mM Tris, pH 7.4. 400 nL 45% PEG Smear Low, 20 mM cobalt (II) chloride added 6 hours prior to harvesting

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.60394 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 24, 2022 / Details: Mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.60394 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 12191 / % possible obs: 98.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.031 / Rrim(I) all: 0.058 / Χ2: 0.747 / Net I/σ(I): 13.5 / Num. measured all: 41552
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.153.40.4436090.8430.2820.5270.73899.5
3.15-3.213.50.3646130.9190.2250.4290.7798.1
3.21-3.273.40.3375890.8740.2190.4040.84197.2
3.27-3.343.50.2635850.9320.1630.3110.8598
3.34-3.413.40.2066170.9430.1340.2470.88699.8
3.41-3.493.30.1676090.9710.1070.20.97599
3.49-3.583.40.1495960.9730.0950.1780.99597.2
3.58-3.683.30.1055890.9810.0690.1260.97797.8
3.68-3.783.10.0865710.9830.0580.1040.90890.5
3.78-3.913.30.075870.990.0440.0830.85695.3
3.91-4.043.60.0616020.9910.0380.0720.868100
4.04-4.213.50.0456240.9930.0280.0530.7799.7
4.21-4.43.50.046180.9950.0250.0480.73499.7
4.4-4.633.60.0356010.9960.0220.0420.68899.7
4.63-4.923.50.0336340.9940.020.0390.67699.4
4.92-5.33.50.0346230.9950.0210.040.54499.7
5.3-5.833.40.0316240.9960.0190.0360.47899.5
5.83-6.673.20.036230.9930.0190.0360.47199.4
6.67-8.393.30.0336000.9960.0210.0390.45592.4
8.39-403.30.0366770.9930.0230.0430.53299.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6WUW

6wuw


Resolution: 3.1→37.18 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.867 / SU B: 50.078 / SU ML: 0.434 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.562 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 582 5.1 %RANDOM
Rwork0.2015 ---
obs0.2044 10788 93.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 161.32 Å2 / Biso mean: 64.265 Å2 / Biso min: 11.53 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å20 Å21.45 Å2
2--0.64 Å20 Å2
3---0.79 Å2
Refinement stepCycle: final / Resolution: 3.1→37.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4622 0 146 43 4811
Biso mean--59.16 36.76 -
Num. residues----584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0124860
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164679
X-RAY DIFFRACTIONr_angle_refined_deg0.9661.6616523
X-RAY DIFFRACTIONr_angle_other_deg0.3281.57510886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5275583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.244524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19310862
X-RAY DIFFRACTIONr_chiral_restr0.0470.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025469
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021011
LS refinement shellResolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 30 -
Rwork0.294 592 -
all-622 -
obs--70.84 %
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)
115.01693.0704-5.33617.27450.5573.23590.13440.05240.02330.04950.0893-1.0869-0.41580.3855-0.22380.366-0.0981-0.08110.2189-0.11160.454851.80120.53423.493
23.53783.06982.09167.22180.58451.60360.09520.3067-0.3057-0.0932-0.145-0.57020.07710.30090.04970.5198-0.08490.06030.343-0.13130.735657.07111.32223.41
343.826511.8126-34.05323.089-4.210627.70860.3591-0.2523-1.44120.7201-1.85661.3888-0.0988-0.25891.49750.5163-0.1016-0.19450.3116-0.06350.666941.7124.47424.159
41.64520.40010.58956.01585.35938.3455-0.1112-0.0110.11110.3460.01260.2135-0.4172-0.27350.09860.40110.005-0.01790.03510.01820.024734.89724.92733.268
56.0638-1.31831.69362.6597-0.88766.45570.18510.90410.0560.0529-0.2068-0.2468-0.87120.55580.02170.3439-0.0180.01560.15030.00710.025432.26224.9842.58
63.4027-0.1694-1.04212.4556-1.88456.32840.14210.2986-0.59210.12610.10320.2728-0.1353-0.3506-0.24530.16870.0347-0.09070.0398-0.03920.184812.32917.8579.581
712.72973.53281.19923.62035.1849.1338-0.2535-3.1139-1.5418-0.07650.165-0.3038-0.27041.36990.08841.18840.4380.10271.490.6170.53867.68714.18542.862
85.5772.684-1.8123.1625-0.246410.09350.2405-1.20480.05060.0882-0.44620.3892-1.0728-0.68290.20570.6380.20770.05610.78930.28820.2896-2.1615.64841.753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 38
2X-RAY DIFFRACTION2A39 - 100
3X-RAY DIFFRACTION3A101 - 111
4X-RAY DIFFRACTION4A112 - 196
5X-RAY DIFFRACTION5A197 - 316
6X-RAY DIFFRACTION6A317 - 498
7X-RAY DIFFRACTION7A499 - 524
8X-RAY DIFFRACTION8A525 - 584

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