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- PDB-3sqj: Recombinant human serum albumin from transgenic plant -

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Basic information

Entry
Database: PDB / ID: 3sqj
TitleRecombinant human serum albumin from transgenic plant
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / recombinant human serum albumin / myristic acid / transgenic rice / serum albumin
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; 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
MYRISTIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHe, Y. / Yang, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Large-scale production of functional human serum albumin from transgenic rice seeds.
Authors: He, Y. / Ning, T. / Xie, T. / Qiu, Q. / Zhang, L. / Sun, Y. / Jiang, D. / Fu, K. / Yin, F. / Zhang, W. / Shen, L. / Wang, H. / Li, J. / Lin, Q. / Sun, Y. / Li, H. / Zhu, Y. / Yang, D.
History
DepositionJul 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Sep 13, 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
Revision 1.4Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,96917
Polymers132,5442
Non-polymers3,42615
Water10,016556
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0999
Polymers66,2721
Non-polymers1,8278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8708
Polymers66,2721
Non-polymers1,5997
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.610, 38.368, 184.037
Angle α, β, γ (deg.)90.000, 104.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serum albumin


Mass: 66271.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, HSA, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Oryza sativa (Asian cultivated rice) / References: UniProt: P02768
#2: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C14H28O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28% PEG 3350, 50mM phosphate, 150 mM KCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.05→47.8 Å / Num. obs: 82055 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rsym value: 0.064 / Net I/σ(I): 24.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BJ5

1bj5


Resolution: 2.05→47.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.257 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3026 4112 5 %RANDOM
Rwork0.2346 ---
obs0.238 82054 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 82.59 Å2 / Biso mean: 38.6929 Å2 / Biso min: 16.55 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20.04 Å2
2--1.11 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9095 0 218 556 9869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0229512
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.98212819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78851162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32824.815432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.627151613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.141546
X-RAY DIFFRACTIONr_chiral_restr0.1250.21412
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217076
X-RAY DIFFRACTIONr_mcbond_it1.061.55842
X-RAY DIFFRACTIONr_mcangle_it1.89529385
X-RAY DIFFRACTIONr_scbond_it3.15633670
X-RAY DIFFRACTIONr_scangle_it5.1414.53434
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 286 -
Rwork0.285 5708 -
all-5994 -
obs--99.44 %

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