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- PDB-8ew4: Human Serum Albumin with Cobalt (II) and Myristic Acid - crystal 1 -

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Basic information

Entry
Database: PDB / ID: 8ew4
TitleHuman Serum Albumin with Cobalt (II) and Myristic Acid - crystal 1
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


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 / small molecule 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/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
Similarity search - Domain/homology
: / MYRISTIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsGucwa, M. / Cooper, D.R. / Unciano, J. / Lea, K. / Kim, L. / Lenkiewicz, J. / Starban, I. / 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 21, 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 / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _entity.pdbx_number_of_molecules / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _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 / _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_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 / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length
Description: Polymer geometry
Details: We manage to improve clashscore, and sidechain outliers. Also, the water ligands in metalsites were improved.
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

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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)69,09115
Polymers66,5711
Non-polymers2,51914
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.775, 38.503, 95.865
Angle α, β, γ (deg.)90.000, 103.550, 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.: 4 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47 % / 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 myristic acid, 50 mM sodium chloride, 25 mM Tris, pH 7.4. 400 nL 45% PEG Smear Low, 20 ...Details: 200 nL 22.5% PEG Smear Low, 10% isopropanol, 100 mM Tris, pH 7.4 + 200 nL 88 mg/mL albumin, saturated myristic acid, 50 mM sodium chloride, 25 mM Tris, pH 7.4. 400 nL 45% PEG Smear Low, 20 mM cobalt 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: 2.4→40 Å / Num. obs: 24101 / % possible obs: 97.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.034 / Rrim(I) all: 0.063 / Χ2: 0.78 / Net I/σ(I): 14.1 / Num. measured all: 79931
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.443.20.27711290.9550.1770.330.73993.5
2.44-2.493.40.24411820.9530.1540.290.73796.6
2.49-2.533.40.22512140.9660.1420.2670.80298.7
2.53-2.593.40.19411940.9710.1230.230.78497
2.59-2.643.40.17811970.9710.1140.2120.77998.8
2.64-2.73.30.14512020.9790.0930.1730.7997.6
2.7-2.773.30.12112010.9840.0770.1440.78197.9
2.77-2.853.40.10511890.9860.0670.1260.78198.2
2.85-2.933.20.0912270.9890.0590.1080.77599.1
2.93-3.023.30.08112210.990.0520.0970.81298.3
3.02-3.133.20.06711760.9920.0440.080.78697.8
3.13-3.2630.05711170.9910.0390.0690.77189.1
3.26-3.413.40.05711940.990.0360.0670.80897.2
3.41-3.583.50.05412310.9930.0340.0640.82798.9
3.58-3.813.50.05212410.9910.0330.0610.85699.6
3.81-4.13.40.04912320.9930.0310.0580.85899.4
4.1-4.523.40.04512410.9940.0290.0540.78899.5
4.52-5.173.30.04412470.9930.0280.0520.76598.6
5.17-6.5130.03911740.9930.0260.0470.64191.6
6.51-403.40.04212920.9940.0270.0510.67797.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6WUW

6wuw


Resolution: 2.4→37.56 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.894 / SU B: 21.53 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.879 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2621 1118 4.9 %RANDOM
Rwork0.2032 ---
obs0.2061 21539 92.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.57 Å2 / Biso mean: 40.738 Å2 / Biso min: 11.54 Å2
Baniso -1Baniso -2Baniso -3
1--2.07 Å2-0 Å2-0.57 Å2
2--0.03 Å20 Å2
3---2.07 Å2
Refinement stepCycle: final / Resolution: 2.4→37.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4643 0 164 161 4968
Biso mean--42.23 34.49 -
Num. residues----584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0124900
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164747
X-RAY DIFFRACTIONr_angle_refined_deg0.8911.6626568
X-RAY DIFFRACTIONr_angle_other_deg0.3071.57511052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6755583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.46524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19810873
X-RAY DIFFRACTIONr_chiral_restr0.0490.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021018
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 68 -
Rwork0.257 1110 -
all-1178 -
obs--66.7 %
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)
17.1260.3706-2.13.9403-0.87152.104-0.0765-0.0203-0.0948-0.04530.1018-0.8163-0.04720.4691-0.02530.2781-0.06550.12570.1822-0.11120.242153.96919.8626.59
25.921-1.5497-0.37664.6681-0.26114.37030.3236-0.1675-0.07540.1023-0.28280.10410.35870.1523-0.04080.3339-0.04380.06870.0374-0.00990.10949.0884.14425.588
31.1164-0.9115-0.83432.57632.61556.6156-0.00980.02290.06940.0551-0.11110.153-0.3776-0.33460.12090.2844-0.03680.11610.1164-0.03410.076732.53524.48134.597
43.04860.12791.32822.3552-0.92053.9448-0.01840.324-0.031-0.20030.0133-0.1919-0.17620.43380.00510.4354-0.04020.150.1844-0.02810.060334.49624.2776.768
52.88420.5676-0.39861.80251.79855.0266-0.07630.4970.0383-0.41680.0150.2391-0.4699-0.35910.06140.40340.06380.00390.21290.00310.058115.50821.538-8.269
62.12480.4768-1.49094.1738-1.1046.59880.1503-0.2444-0.0801-0.08180.0516-0.0404-0.30120.2467-0.20190.2132-0.05060.05780.155-0.03550.03910.69418.56921.764
72.61841.2679-1.01751.9588-1.78397.45050.1024-0.5426-0.17520.0894-0.058-0.01940.4267-0.0996-0.04440.13610.00370.02240.16510.06070.02785.79212.47332.181
85.14274.39846.44155.23144.756818.71310.0319-0.61460.51620.0748-0.27080.3144-0.9598-0.84330.2390.20510.06670.07490.5882-0.07660.0934-3.91818.52144.731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 65
2X-RAY DIFFRACTION2A66 - 110
3X-RAY DIFFRACTION3A111 - 196
4X-RAY DIFFRACTION4A197 - 297
5X-RAY DIFFRACTION5A298 - 386
6X-RAY DIFFRACTION6A387 - 478
7X-RAY DIFFRACTION7A479 - 537
8X-RAY DIFFRACTION8A538 - 584

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