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- PDB-8ew7: Human Serum Albumin with Cobalt (II) and Myristic Acid - crystal 2 -

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Basic information

Entry
Database: PDB / ID: 8ew7
TitleHuman Serum Albumin with Cobalt (II) and Myristic Acid - crystal 2
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


exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / 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/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: 3.3 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 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 / entity ...atom_site / entity / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_conn
Item: _entity.pdbx_number_of_molecules / _pdbx_poly_seq_scheme.auth_mon_id ..._entity.pdbx_number_of_molecules / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_validate_planes.auth_seq_id / _pdbx_validate_planes.rmsd / _refine.B_iso_max / _refine.B_iso_mean / _refine.aniso_B[1][1] / _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_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_hist.pdbx_number_residues_total / _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
Description: Polymer geometry
Details: We improved clashscore, ramachandran outliers, sidechain outliers. The water molecule ligands in metals sites were also 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
Revision 2.4Oct 23, 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)67,78713
Polymers66,5711
Non-polymers1,21612
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-48 kcal/mol
Surface area28450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.104, 38.301, 96.719
Angle α, β, γ (deg.)90.000, 105.040, 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.: 9 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.23 Å3/Da / Density % sol: 44 % / Description: Rectangular prisms
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 200 nL 18% PEG3350, 50 mM Tris, pH 7.4 + 200 nL 50 mg/mL albumin, 50% saturated myristic acid, 50 mM sodium chloride, 25 mM Tris, pH 7.4. Addition of 40% PEG3350, 50 mM Tris, 20 mM cobalt ...Details: 200 nL 18% PEG3350, 50 mM Tris, pH 7.4 + 200 nL 50 mg/mL albumin, 50% saturated myristic acid, 50 mM sodium chloride, 25 mM Tris, pH 7.4. Addition of 40% PEG3350, 50 mM Tris, 20 mM cobalt (II) chloride 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: 19-ID / Wavelength: 1.60311 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2022 / Details: Sagittal focusing
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.60311 Å / Relative weight: 1
ReflectionResolution: 3.3→40 Å / Num. obs: 9385 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.052 / Rrim(I) all: 0.134 / Χ2: 0.907 / Net I/σ(I): 5 / Num. measured all: 61539
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.366.60.5644610.9210.2380.6140.818100
3.36-3.426.70.6084540.9160.2560.6610.82199.8
3.42-3.486.40.4464720.9260.190.4860.83100
3.48-3.556.60.4184540.9310.1780.4550.878100
3.55-3.636.30.3714570.9480.1610.4050.96599.8
3.63-3.726.10.334550.9820.1440.3611.02499.8
3.72-3.816.70.314700.9510.1320.3370.964100
3.81-3.916.80.254800.9670.1030.2710.966100
3.91-4.036.80.2134460.9810.0880.2310.998100
4.03-4.166.80.1874640.9850.0780.2041.088100
4.16-4.316.70.1684840.9870.070.1821.10699.8
4.31-4.486.70.1444450.990.060.1571.01899.6
4.48-4.686.30.1334800.9870.0580.1461.12399.8
4.68-4.936.30.124670.990.0510.1311.02999.8
4.93-5.2470.1144650.9930.0470.1240.924100
5.24-5.646.80.124840.9910.0490.130.865100
5.64-6.26.70.1114680.9920.0460.120.7799.8
6.2-7.160.0864750.9910.0380.0940.746100
7.1-8.936.70.0544890.9970.0220.0580.661100
8.93-406.10.0465150.9970.020.050.5699.2

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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: 3.3→37.28 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.832 / SU B: 32.636 / SU ML: 0.531 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.699 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.272 429 4.9 %RANDOM
Rwork0.1886 ---
obs0.1927 8345 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.2 Å2 / Biso mean: 44.521 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å20.43 Å2
2---0.88 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: final / Resolution: 3.3→37.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4621 0 57 44 4722
Biso mean--51.68 20.27 -
Num. residues----583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0124773
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164538
X-RAY DIFFRACTIONr_angle_refined_deg1.0211.6586435
X-RAY DIFFRACTIONr_angle_other_deg0.4231.57810540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1925582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.699523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36810865
X-RAY DIFFRACTIONr_chiral_restr0.050.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025432
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021012
LS refinement shellResolution: 3.3→3.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 17 -
Rwork0.291 395 -
all-412 -
obs--60.95 %

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