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- PDB-4g03: High-resolution Crystal Structural Variance Analysis between Reco... -

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Basic information

Entry
Database: PDB / ID: 4g03
TitleHigh-resolution Crystal Structural Variance Analysis between Recombinant and Wild-type Human Serum Albumin
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN
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: 2.216 Å
AuthorsCao, H.L. / Yin, D.C.
CitationJournal: To be Published
Title: High-resolution Crystal Structural Variance Analysis between Recombinant and Wild-type Human Serum Albumin
Authors: Cao, H.L. / Yin, D.C.
History
DepositionJul 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water1,45981
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
MethodPISA
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
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.570, 58.670, 95.675
Angle α, β, γ (deg.)75.71, 88.07, 73.63
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
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02768
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 28-30% (w/v) PEG 3350, Sigma-Aldrich, 50mM potassium phosphate, pH 7.0, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 24, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.216→47.219 Å / Num. obs: 58401 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 23.337
Reflection shellResolution: 2.23→2.27 Å / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AO6

1ao6


Resolution: 2.216→47.219 Å / SU ML: 0.34 / σ(F): 1.96 / Phase error: 33.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3014 1999 3.52 %
Rwork0.2359 --
obs0.2382 56802 96.55 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.201 Å2 / ksol: 0.297 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6603 Å2-0.6885 Å2-7.0533 Å2
2--0.1727 Å27.8091 Å2
3----0.833 Å2
Refinement stepCycle: LAST / Resolution: 2.216→47.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9198 0 0 81 9279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089410
X-RAY DIFFRACTIONf_angle_d1.09812648
X-RAY DIFFRACTIONf_dihedral_angle_d16.6473558
X-RAY DIFFRACTIONf_chiral_restr0.0781406
X-RAY DIFFRACTIONf_plane_restr0.0051648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2155-2.27090.3531170.28663562X-RAY DIFFRACTION87
2.2709-2.33230.35351540.27383922X-RAY DIFFRACTION97
2.3323-2.4010.36691380.2623951X-RAY DIFFRACTION97
2.401-2.47850.29921490.25143948X-RAY DIFFRACTION98
2.4785-2.5670.32431430.24673927X-RAY DIFFRACTION97
2.567-2.66980.34731480.25543971X-RAY DIFFRACTION97
2.6698-2.79130.32311420.25633958X-RAY DIFFRACTION98
2.7913-2.93840.32491470.28233961X-RAY DIFFRACTION98
2.9384-3.12250.33891420.26693950X-RAY DIFFRACTION98
3.1225-3.36350.351420.26643967X-RAY DIFFRACTION98
3.3635-3.70190.31181490.24533977X-RAY DIFFRACTION98
3.7019-4.23730.28291480.21363929X-RAY DIFFRACTION97
4.2373-5.33740.26981350.19843891X-RAY DIFFRACTION96
5.3374-47.22980.25131450.21173889X-RAY DIFFRACTION96

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