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- PDB-7a9c: Human serum albumin (HSA) crystallized in the presence of yttrium... -

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Basic information

Entry
Database: PDB / ID: 7a9c
TitleHuman serum albumin (HSA) crystallized in the presence of yttrium (III) chloride
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / human serum albumin complexed with Y3+
Function / homology
Function and homology information


exogenous protein binding / Ciprofloxacin ADME / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / 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 / 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
YTTRIUM (III) ION / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsZocher, G. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Cryst.Growth Des. / Year: 2020
Title: Protein Crystallization in the Presence of a Metastable Liquid-Liquid Phase Separation
Authors: Maier, R. / Zocher, G. / Sauter, A. / Da Vela, S. / Matsarskaia, O. / Schweins, R. / Sztucki, M. / Zhang, F. / Stehle, T. / Schreiber, F.
History
DepositionSep 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 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

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Assembly

Deposited unit
AAA: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7213
Polymers66,5431
Non-polymers1782
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-10 kcal/mol
Surface area29870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.270, 71.930, 180.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Albumin


Mass: 66543.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF ...Details: MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV AASQAALGL
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Homo sapiens (human) / References: UniProt: P02768
#2: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Y / Feature type: SUBJECT OF INVESTIGATION
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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 293 K / Method: batch mode / Details: 2mM yttrium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.7 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2009
RadiationMonochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.75→40 Å / Num. obs: 35814 / % possible obs: 99.5 % / Redundancy: 16.2 % / Biso Wilson estimate: 75.7 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.8
Reflection shellResolution: 2.75→2.82 Å / Num. unique obs: 2442 / CC1/2: 0.641 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0232 2018/13/08refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BXI

2bxi


Resolution: 2.75→30.002 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / SU B: 19.86 / SU ML: 0.379 / Cross valid method: FREE R-VALUE / ESU R Free: 0.423
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2946 1540 -
Rwork0.2385 17702 -
all0.243 --
obs-19242 99.319 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 79.473 Å2
Baniso -1Baniso -2Baniso -3
1--1.112 Å2-0 Å2-0 Å2
2--5.641 Å2-0 Å2
3----4.529 Å2
Refinement stepCycle: LAST / Resolution: 2.75→30.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4535 0 2 0 4537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0134641
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174249
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.656285
X-RAY DIFFRACTIONr_angle_other_deg1.0981.5779887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0695581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70123.233232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.19815813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2251523
X-RAY DIFFRACTIONr_chiral_restr0.0430.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02935
X-RAY DIFFRACTIONr_nbd_refined0.20.21081
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.23797
X-RAY DIFFRACTIONr_nbtor_refined0.1550.22197
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22353
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2107
X-RAY DIFFRACTIONr_metal_ion_refined0.3880.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4340.215
X-RAY DIFFRACTIONr_nbd_other0.1690.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2230.23
X-RAY DIFFRACTIONr_mcbond_it5.52917.1342327
X-RAY DIFFRACTIONr_mcbond_other5.51717.1362325
X-RAY DIFFRACTIONr_mcangle_it8.28825.7342907
X-RAY DIFFRACTIONr_mcangle_other8.28225.7332907
X-RAY DIFFRACTIONr_scbond_it5.54717.6872314
X-RAY DIFFRACTIONr_scbond_other5.54617.6852315
X-RAY DIFFRACTIONr_scangle_it8.53726.2013378
X-RAY DIFFRACTIONr_scangle_other8.53626.23379
X-RAY DIFFRACTIONr_lrange_it13.751161.60718655
X-RAY DIFFRACTIONr_lrange_other13.752161.60718651
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.75-2.8210.4111010.3831164136192.94640.368
2.821-2.8970.3991090.3531254137599.12730.323
2.897-2.9810.3631040.313119613001000.281
2.981-3.0710.3921050.315120313081000.285
3.071-3.1710.302980.268113012281000.234
3.171-3.2810.3661000.267114412441000.231
3.281-3.4030.309920.279106511571000.25
3.403-3.540.372910.264104311341000.242
3.54-3.6950.296870.25299710841000.229
3.695-3.8730.339830.24195610391000.226
3.873-4.0790.274790.2419149931000.221
4.079-4.3210.263770.1928829591000.183
4.321-4.6130.288720.1968238951000.189
4.613-4.9720.243660.2027658311000.196
4.972-5.4320.271630.2337177801000.221
5.432-6.0480.327570.2766667231000.261
6.048-6.9370.324510.25658763999.84350.248
6.937-8.3850.254440.1935005441000.206
8.385-11.4210.174360.1544194551000.178
11.421-30.0020.304250.2632773021000.301

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