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- PDB-3jry: Human Serum albumin with bound Sulfate -

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Basic information

Entry
Database: PDB / ID: 3jry
TitleHuman Serum albumin with bound Sulfate
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / ALBUMIN / SULFATE / CARRIER PROTEIN / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Glycation / Glycoprotein / Lipid-binding / Metal-binding / Phosphoprotein / Secreted
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 / nucleus / identical protein binding / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHein, K.L. / Kragh-Hansen, U. / Morth, J.P. / Nissen, P.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Crystallographic analysis reveals a unique lidocaine binding site on human serum albumin.
Authors: Hein, K.L. / Kragh-Hansen, U. / Morth, J.P. / Jeppesen, M.D. / Otzen, D. / Moller, J.V. / Nissen, P.
History
DepositionSep 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 4, 2013Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,3354
Polymers133,1422
Non-polymers1922
Water8,251458
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6672
Polymers66,5711
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6672
Polymers66,5711
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.600, 55.787, 121.344
Angle α, β, γ (deg.)80.48, 90.75, 63.48
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:196)
211chain B and (resseq 1:196)
112chain A and (resseq 197:388)
212chain B and (resseq 197:388)
113chain A and (resseq 389:582)
213chain B and (resseq 389:582)

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Serum albumin /


Mass: 66571.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: PICHIA PASTORIS (fungus) / References: UniProt: P02768
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22-25% PEG 3350, 100-200mM ammonium sulphate and 50mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.915 Å
DetectorDate: Jan 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 2.3→120 Å / Num. all: 56941 / Num. obs: 51888 / % possible obs: 91.1 % / Observed criterion σ(I): 2 / Redundancy: 1.86 % / Biso Wilson estimate: 41.8 Å2 / Rsym value: 0.041 / Net I/σ(I): 13.46
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.73 % / Mean I/σ(I) obs: 3.41 / Num. unique all: 5840 / Rsym value: 0.238 / % possible all: 23.8

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AO6
Resolution: 2.3→27.753 Å / SU ML: 0.26 / σ(F): 1.99 / Phase error: 29.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2681 2645 5.1 %
Rwork0.2092 --
obs0.2123 51876 91.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.815 Å2 / ksol: 0.322 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3456 Å2-5.3621 Å21.4873 Å2
2---0.1415 Å2-1.047 Å2
3---0.487 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9118 0 10 458 9586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089336
X-RAY DIFFRACTIONf_angle_d0.98312550
X-RAY DIFFRACTIONf_dihedral_angle_d16.4423486
X-RAY DIFFRACTIONf_chiral_restr0.071394
X-RAY DIFFRACTIONf_plane_restr0.0041636
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1524X-RAY DIFFRACTIONPOSITIONAL
12B1524X-RAY DIFFRACTIONPOSITIONAL0.044
21A1526X-RAY DIFFRACTIONPOSITIONAL
22B1526X-RAY DIFFRACTIONPOSITIONAL0.033
31A1509X-RAY DIFFRACTIONPOSITIONAL
32B1509X-RAY DIFFRACTIONPOSITIONAL0.032
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.34180.31041170.2353233981
2.3418-2.38680.29791360.2244249389
2.3868-2.43550.30821260.2283256188
2.4355-2.48850.30861180.2154251190
2.4885-2.54630.34021470.2086260390
2.5463-2.60990.28071430.2168254692
2.6099-2.68050.33191370.2203262891
2.6805-2.75930.34061310.2378258592
2.7593-2.84820.28661490.2276264092
2.8482-2.94990.31191350.2335265592
2.9499-3.06790.28051490.2441263994
3.0679-3.20730.35081460.2386264094
3.2073-3.37620.28491670.2304260893
3.3762-3.58730.25621270.213266893
3.5873-3.86360.26631350.1945261292
3.8636-4.25110.22111480.1784261692
4.2511-4.86340.21221480.1589262893
4.8634-6.11660.23031480.1771261192
6.1166-27.75530.19581380.171264893
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9414-0.4163-0.50990.77380.80521.59-0.06140.0918-0.1438-0.13420.0879-0.0187-0.0939-0.21940.19590.1177-0.04520.02810.2182-0.03730.0345-26.8204-36.7628-46.3901
20.72760.35190.34621.37431.92611.11820.1068-0.30050.03590.1745-0.19290.16950.0833-0.1950.06160.3152-0.07110.03020.25710.01570.0745-31.7915-29.213145.396
31.3488-0.0992-0.69080.9149-0.01330.72540.21040.17110.2735-0.1431-0.029-0.0318-0.0552-0.1137-0.1470.06740.050.01470.11810.05170.1215-41.1755-13.3012-28.051
40.67530.42960.25371.48660.75331.13680.1396-0.0235-0.19860.38960.1503-0.48110.26070.0455-0.25130.2084-0.0057-0.10610.0617-0.00480.2595-17.2007-52.782527.4251
51.37320.42850.39410.5235-0.56690.4280.06810.1522-0.0945-0.0109-0.1168-0.14530.04560.01820.04420.08170.01730.00410.1488-0.00760.1909-12.9867-30.5643-14.8378
61.43640.75640.39210.905-0.29780.1698-0.09120.02360.23480.22060.0547-0.0255-0.1306-0.0320.03880.2286-0.0062-0.01860.0848-0.01580.2074-19.734-19.757314.115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND (RESSEQ 389:582)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 1:196)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 197:388)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 197:388)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 389:582)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 389:582)

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