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- PDB-5z0b: Crystal structure of plasma-derived human serum albumin -

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Basic information

Entry
Database: PDB / ID: 5z0b
TitleCrystal structure of plasma-derived human serum albumin
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Human serum albumin
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
LINOLEIC ACID / OCTANOIC ACID (CAPRYLIC ACID) / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PALMITIC ACID / TRYPTOPHAN / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsPark, J. / Kim, M.-S. / Shin, D.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2015R1D1A1A01058942 Korea, Republic Of
CitationJournal: To Be Published
Title: The crystal structure of plasma-derived human serum albumin
Authors: Park, J. / Kim, M.S. / Shin, D.H.
History
DepositionDec 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 2.0Jun 24, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / chem_comp / computing / diffrn / entity / pdbx_audit_support / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_site / struct_site_gen / symmetry
Item: _cell.angle_beta / _cell.volume ..._cell.angle_beta / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn.pdbx_serial_crystal_experiment / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_all / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_high / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _software.version / _struct_mon_prot_cis.pdbx_omega_angle / _symmetry.space_group_name_Hall
Description: Ligand geometry
Details: We have replaced several fatty acid ligands with longer fatty acids, re-modeled the ligand geometry, and refined the overall protein structure.
Provider: author / Type: Coordinate replacement
Revision 2.1Nov 22, 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
B: Serum albumin
C: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,97760
Polymers199,7623
Non-polymers8,21657
Water8,305461
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21180 Å2
ΔGint-160 kcal/mol
Surface area76450 Å2
Unit cell
Length a, b, c (Å)203.576, 113.466, 86.809
Angle α, β, γ (deg.)90.000, 104.878, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Serum albumin /


Mass: 66587.219 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768

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Non-polymers , 10 types, 518 molecules

#2: Chemical ChemComp-EIC / LINOLEIC ACID / 9,12-LINOLEIC ACID / Linoleic acid


Mass: 280.445 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID) / Caprylic acid


Mass: 144.211 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H16O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: SO4
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 49.99 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG600, Ammonium sulfate, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9536 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.17→19.78 Å / Num. obs: 96299 / % possible obs: 96.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 35.86 Å2 / Rsym value: 0.053 / Net I/σ(I): 10.8
Reflection shellResolution: 2.17→2.29 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 11416 / Rsym value: 0.29 / % possible all: 78.3

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AO6

1ao6


Resolution: 2.17→19.78 Å / SU ML: 0.258 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.3239
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2323 4822 5.01 %
Rwork0.1828 91467 -
obs0.1853 96289 96.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.61 Å2
Refinement stepCycle: LAST / Resolution: 2.17→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13495 0 534 461 14490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007714268
X-RAY DIFFRACTIONf_angle_d0.914319109
X-RAY DIFFRACTIONf_chiral_restr0.04432067
X-RAY DIFFRACTIONf_plane_restr0.0072440
X-RAY DIFFRACTIONf_dihedral_angle_d17.4175644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.20.2775960.25251954X-RAY DIFFRACTION61.36
2.2-2.220.30521200.22582386X-RAY DIFFRACTION75.26
2.22-2.250.25741170.22132540X-RAY DIFFRACTION80.64
2.25-2.280.27291580.21672785X-RAY DIFFRACTION88.46
2.28-2.310.28471710.21093060X-RAY DIFFRACTION97.85
2.31-2.340.25041740.20383147X-RAY DIFFRACTION98.93
2.34-2.370.23361550.19873081X-RAY DIFFRACTION98.69
2.37-2.410.23651600.19493155X-RAY DIFFRACTION98.98
2.41-2.450.27021440.20123119X-RAY DIFFRACTION98.97
2.45-2.490.25471460.19823176X-RAY DIFFRACTION98.96
2.49-2.530.25781720.19993129X-RAY DIFFRACTION99.01
2.53-2.580.26671440.20013141X-RAY DIFFRACTION99.07
2.58-2.630.2721790.19613126X-RAY DIFFRACTION99.07
2.63-2.680.25111850.19653099X-RAY DIFFRACTION99.21
2.68-2.740.23121370.193154X-RAY DIFFRACTION99.1
2.74-2.80.24611740.20133174X-RAY DIFFRACTION99.23
2.8-2.870.25161770.19753089X-RAY DIFFRACTION99.15
2.87-2.950.24631750.20473123X-RAY DIFFRACTION99.34
2.95-3.030.2591460.20213165X-RAY DIFFRACTION99.43
3.03-3.130.27071550.20363175X-RAY DIFFRACTION99.34
3.13-3.240.2571670.19553172X-RAY DIFFRACTION99.38
3.24-3.370.25251460.19243153X-RAY DIFFRACTION99.49
3.37-3.530.22931700.17723149X-RAY DIFFRACTION99.55
3.53-3.710.21911990.16973116X-RAY DIFFRACTION99.49
3.71-3.940.20341940.16693156X-RAY DIFFRACTION99.7
3.94-4.240.20331700.15333163X-RAY DIFFRACTION99.55
4.24-4.660.20621580.15133193X-RAY DIFFRACTION99.73
4.66-5.330.22541870.1643170X-RAY DIFFRACTION99.76
5.33-6.670.22651700.19583205X-RAY DIFFRACTION99.94
6.67-19.780.20441760.16983212X-RAY DIFFRACTION99.01
Refinement TLS params.Method: refined / Origin x: 39.4380300071 Å / Origin y: -8.39593435405 Å / Origin z: -18.2087829151 Å
111213212223313233
T0.358170978783 Å2-0.00734545067059 Å20.00443158604637 Å2-0.356259378784 Å2-0.025069542985 Å2--0.304270145083 Å2
L0.183653343441 °20.0579389621211 °20.0173917792905 °2-0.289964508204 °2-0.105662211305 °2--0.0334615613146 °2
S-0.0284112655503 Å °0.0643034805569 Å °0.0113985798518 Å °-0.0854270752174 Å °0.000789223832073 Å °-0.0085150038951 Å °0.012200153297 Å °-0.0217686084264 Å °1.87666820287E-13 Å °
Refinement TLS groupSelection details: all

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