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- PDB-8a9q: Computational design of stable mammalian serum albumins for bacte... -

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Basic information

Entry
Database: PDB / ID: 8a9q
TitleComputational design of stable mammalian serum albumins for bacterial expression
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / Complex with Warfarin
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
LAURIC ACID / MYRISTIC ACID / R-WARFARIN / Albumin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKhersonsky, O. / Dym, O. / Fleishman, J.S.
Funding support Israel, European Union, 2items
OrganizationGrant numberCountry
Israel Science Foundation1844/19 Israel
European Research Council (ERC)815379European Union
Citation
Journal: J.Mol.Biol. / Year: 2023
Title: Stable Mammalian Serum Albumins Designed for Bacterial Expression.
Authors: Khersonsky, O. / Goldsmith, M. / Zaretsky, I. / Hamer-Rogotner, S. / Dym, O. / Unger, T. / Yona, M. / Fridmann-Sirkis, Y. / Fleishman, S.J.
#1: Journal: Biorxiv / Year: 2023
Title: Stable mammalian serum albumins designed for bacterial expression
Authors: Khersonsky, O. / Goldsmith, M. / Zaretsky, I. / Rogotner, S. / Dym, O. / Unger, T. / Yona, M. / Fleishman, S.J.
History
DepositionJun 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Jul 19, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Sep 20, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Oct 11, 2023Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.type
Revision 1.5Feb 14, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Albumin
B: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,87412
Polymers133,4592
Non-polymers2,41610
Water1,63991
1
A: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9516
Polymers66,7291
Non-polymers1,2225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9236
Polymers66,7291
Non-polymers1,1945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.260, 92.128, 95.553
Angle α, β, γ (deg.)74.35, 89.29, 79.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Albumin


Mass: 66729.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Few designed mutations / Source: (gene. exp.) Escherichia coli (E. coli)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Escherichia coli (E. coli) / References: UniProt: P02768
#2: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-RWF / R-WARFARIN


Mass: 308.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: .05M NaCl, 10% PEG 4000 and 0.05 Tris pH=8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→46.02 Å / Num. obs: 74409 / % possible obs: 89.1 % / Redundancy: 1.5 % / Biso Wilson estimate: 41.82 Å2 / CC1/2: 0.945 / CC star: 0.986 / Rmerge(I) obs: 0.05816 / Rpim(I) all: 0.05186 / Rrim(I) all: 0.08224 / Net I/σ(I): 18.11
Reflection shellResolution: 2→2.071 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.2589 / Num. unique obs: 7010 / CC1/2: 0.86 / Rpim(I) all: 0.2589 / Rrim(I) all: 0.3661 / % possible all: 84.48

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Processing

Software
NameVersionClassification
PHENIX1.15.2refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HSC

6hsc
PDB Unreleased entry


Resolution: 2→46.02 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 14.224 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27066 3634 4.9 %RANDOM
Rwork0.22031 ---
obs0.2228 70736 89.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.111 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.03 Å2-0.08 Å2
2--0.69 Å2-0.7 Å2
3----0.97 Å2
Refinement stepCycle: 1 / Resolution: 2→46.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8896 0 172 91 9159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0139286
X-RAY DIFFRACTIONr_bond_other_d0.0030.0168612
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.66412576
X-RAY DIFFRACTIONr_angle_other_deg1.5251.62219873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77851164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.69622.953430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.088151505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8071543
X-RAY DIFFRACTIONr_chiral_restr0.0960.21228
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210404
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022002
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8564.0724657
X-RAY DIFFRACTIONr_mcbond_other2.8534.0714655
X-RAY DIFFRACTIONr_mcangle_it4.0036.0995820
X-RAY DIFFRACTIONr_mcangle_other4.0036.0995820
X-RAY DIFFRACTIONr_scbond_it3.4164.4774629
X-RAY DIFFRACTIONr_scbond_other3.4114.4774627
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1826.5686756
X-RAY DIFFRACTIONr_long_range_B_refined6.59149.25610309
X-RAY DIFFRACTIONr_long_range_B_other6.59249.25210306
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 225 -
Rwork0.305 4893 -
obs--83.57 %

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