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- PDB-7djn: Human Serum Albumin -

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Basic information

Entry
Database: PDB / ID: 7djn
TitleHuman Serum Albumin
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Human Serum Albumin
Function / homology
Function and homology information


Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...Ciprofloxacin ADME / exogenous protein binding / 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 / platelet alpha granule lumen / fatty acid binding / cellular response to starvation / 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 / endoplasmic reticulum lumen / copper ion binding / endoplasmic reticulum / Golgi apparatus / protein-containing complex / extracellular space / DNA binding / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsXiang, W. / Yue, Z. / Su, J.
CitationJournal: To Be Published
Title: Human Serum Albumin
Authors: Xiang, W. / Yue, Z. / Su, J.
History
DepositionNov 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)133,1422
Polymers133,1422
Non-polymers00
Water3,369187
1
A: Serum albumin


Theoretical massNumber of molelcules
Total (without water)66,5711
Polymers66,5711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serum albumin


Theoretical massNumber of molelcules
Total (without water)66,5711
Polymers66,5711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.092, 53.030, 117.424
Angle α, β, γ (deg.)99.170, 93.450, 117.640
Int Tables number1
Space group name H-MP1

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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: Komagataella pastoris (fungus) / References: UniProt: P02768
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.04→19.52 Å / Num. obs: 64942 / % possible obs: 94.2 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.4
Reflection shellResolution: 2.04→2.09 Å / Rmerge(I) obs: 0.973 / Num. unique obs: 4262

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M4R

6m4r


Resolution: 2.04→19.34 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 35.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2759 1971 3.04 %
Rwork0.2419 62932 -
obs0.2429 64903 94.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.32 Å2 / Biso mean: 64.533 Å2 / Biso min: 23.18 Å2
Refinement stepCycle: final / Resolution: 2.04→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8977 0 0 187 9164
Biso mean---54.35 -
Num. residues----1126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.04-2.090.421390.38014398453792
2.09-2.150.38041480.35384452460095
2.15-2.210.35761400.3324481462194
2.21-2.280.37661390.31624497463694
2.28-2.370.38851440.29344587473195
2.37-2.460.36161340.28164483461795
2.46-2.570.31191420.27234547468995
2.57-2.710.28751460.26694513465995
2.71-2.880.28311390.26964554469395
2.88-3.10.34381340.26934554468895
3.1-3.410.31331420.25494480462294
3.41-3.90.23941420.22084495463794
3.9-4.90.21731300.19394471460193
4.9-19.340.21921520.19564420457293
Refinement TLS params.Method: refined / Origin x: 10.476 Å / Origin y: 12.4882 Å / Origin z: -17.3132 Å
111213212223313233
T0.341 Å2-0.1052 Å20.0349 Å2-0.2063 Å20.0204 Å2--0.3171 Å2
L1.0567 °2-0.403 °20.2806 °2-0.4953 °2-0.0504 °2--0.6966 °2
S0.0159 Å °-0.0274 Å °0.0147 Å °-0.0342 Å °-0.0322 Å °0.0294 Å °0.0364 Å °-0.0011 Å °0.0004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 582
2X-RAY DIFFRACTION1allB4 - 582
3X-RAY DIFFRACTION1allS1 - 203

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