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- PDB-8wdd: Crystal structure of BSA in complex with B1 -

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Basic information

Entry
Database: PDB / ID: 8wdd
TitleCrystal structure of BSA in complex with B1
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / Albumin dimer / photo-sensitizer
Function / homology
Function and homology information


cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / fatty acid binding / cellular response to starvation / pyridoxal phosphate binding / protein-containing complex / extracellular space / DNA binding ...cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / fatty acid binding / cellular response to starvation / pyridoxal phosphate binding / protein-containing complex / extracellular space / DNA binding / extracellular region / metal ion binding / 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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsChen, X. / Ge, Y.H. / Yang, H. / Fang, B. / Li, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21807088 China
CitationJournal: To Be Published
Title: Crystal structure of BSA in complex with B1
Authors: Chen, X. / Ge, Y.H. / Yang, H. / Fang, B. / Li, L.
History
DepositionSep 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
A: Albumin
B: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,66811
Polymers133,0642
Non-polymers2,6059
Water00
1
A: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4004
Polymers66,5321
Non-polymers8683
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2687
Polymers66,5321
Non-polymers1,7366
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.822, 45.133, 209.207
Angle α, β, γ (deg.)90.00, 104.50, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Albumin / BSA


Mass: 66531.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ALB / Production host: Bos taurus (domestic cattle) / References: UniProt: P02769
#2: Chemical
ChemComp-VZK / ~{N},~{N}-dimethyl-6-[(~{E})-2-(1-methylpyridin-1-ium-4-yl)ethenyl]naphthalen-2-amine


Mass: 289.394 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C20H21N2 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / Details: 0.2M CaAC2, 22% PEG3350, 0.1M Tris pH6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.9→104.22 Å / Num. obs: 12344 / % possible obs: 98.9 % / Redundancy: 5.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.081 / Rrim(I) all: 0.192 / Net I/σ(I): 8.4
Reflection shellResolution: 3.9→4.36 Å / Redundancy: 6 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 3484 / CC1/2: 0.671 / Rpim(I) all: 0.344 / Rrim(I) all: 0.827 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9→70.587 Å / SU ML: 0.85 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 48.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3701 593 4.82 %
Rwork0.3091 --
obs0.3123 12308 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.9→70.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8457 0 198 0 8655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038840
X-RAY DIFFRACTIONf_angle_d0.57812059
X-RAY DIFFRACTIONf_dihedral_angle_d3.3285280
X-RAY DIFFRACTIONf_chiral_restr0.0371357
X-RAY DIFFRACTIONf_plane_restr0.0051610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9001-4.29250.40711500.34852888X-RAY DIFFRACTION99
4.2925-4.91350.4021420.32362917X-RAY DIFFRACTION99
4.9135-6.190.41691400.3632912X-RAY DIFFRACTION98
6.19-70.5870.33081610.26822998X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -49.147 Å / Origin y: -4.1349 Å / Origin z: -28.2162 Å
111213212223313233
T1.0041 Å20.0415 Å20.2294 Å2-0.7312 Å2-0.0562 Å2--0.8837 Å2
L0.4862 °2-0.2129 °20.4455 °2-0.6782 °20.0113 °2--0.7995 °2
S-0.0613 Å °-0.2451 Å °0.2658 Å °0.1864 Å °0.048 Å °0.0328 Å °-0.0697 Å °-0.2376 Å °0.0042 Å °
Refinement TLS groupSelection details: all

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