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- PDB-4lb2: X-ray study of human serum albumin complexed with idarubicin -

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Basic information

Entry
Database: PDB / ID: 4lb2
TitleX-ray study of human serum albumin complexed with idarubicin
ComponentsSERUM ALBUMIN
KeywordsTRANSPORT PROTEIN / PLASMA PROTEIN / CANCER / ONCOLOGY DRUG COMPLEX
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity / Aspirin ADME / 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 / nucleus / identical protein binding / 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
IDARUBICIN / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWang, Z. / Ho, J.X. / Ruble, J. / Rose, J.P. / Carter, D.C.
Citation
Journal: Biochim.Biophys.Acta / Year: 2013
Title: Structural studies of several clinically important oncology drugs in complex with human serum albumin.
Authors: Wang, Z.M. / Ho, J.X. / Ruble, J.R. / Rose, J. / Ruker, F. / Ellenburg, M. / Murphy, R. / Click, J. / Soistman, E. / Wilkerson, L. / Carter, D.C.
#1: Journal: Burgers medicinal chemistry drug design and development, 7th edition
Year: 2010

Title: Crystallographic survey of albumin drug interaction and preliminary applications in cancer chemotherapy
Authors: Carter, D.C.
#2: Journal: Adv.Protein Chem. / Year: 1994
Title: Structure of Serum Albumin
Authors: Carter, D.C. / Ho, J.X.
#3: Journal: Eur.J.Biochem. / Year: 1994
Title: Preliminary crystallographic studies of four crystal forms of serum albumin.
Authors: Carter, D.C. / Chang, B. / Ho, J.X. / Keeling, K. / Krishnasami, Z.
#4: Journal: Nature / Year: 1993
Title: Erratum. Atomic Structure and Chemistry of Human Serum Albumin
Authors: Ho, X.M. / Carter, D.C.
#5: Journal: Nature / Year: 1992
Title: Atomic structure and chemistry of human serum albumin.
Authors: He, X.M. / Carter, D.C.
#6: Journal: Science / Year: 1990
Title: Structure of Human Serum Albumin
Authors: Carter, D.C. / Ho, X.M.
#7: Journal: Science / Year: 1989
Title: Three-dimensional structure of human serum albumin.
Authors: Carter, D.C. / He, X.M. / Munson, S.H. / Twigg, P.D. / Gernert, K.M. / Broom, M.B. / Miller, T.Y.
History
DepositionJun 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Feb 19, 2014Group: Other

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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)135,1326
Polymers133,1422
Non-polymers1,9904
Water1,35175
1
A: SERUM ALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5663
Polymers66,5711
Non-polymers9952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SERUM ALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5663
Polymers66,5711
Non-polymers9952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.952, 58.199, 96.085
Angle α, β, γ (deg.)74.740, 88.630, 76.580
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain B and segid HSB)
NCS domain segments: (Selection details: chain 'B' and segid 'HSB ')

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Components

#1: Protein SERUM ALBUMIN /


Mass: 66571.219 Da / Num. of mol.: 2 / Fragment: UNP residues 25-609 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768
#2: Chemical
ChemComp-DM5 / IDARUBICIN / 4-DEMETHOXY-DAUNORUBICIN / Idarubicin


Mass: 497.494 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H27NO9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350, POTASSIUM PHOSPHATE, Crystals of the complexes were obtained by standard vapor equilibration methods with conditions optimized by screens varying protein concentration, pH, drug ...Details: PEG 3350, POTASSIUM PHOSPHATE, Crystals of the complexes were obtained by standard vapor equilibration methods with conditions optimized by screens varying protein concentration, pH, drug molar ratios, centered on the original crystallization hit using protocols described previously for the monoclinic [Carter, et al., Eur. J. Biochemistry (1994) 226: 1049-1052] and triclinic [Sugo, et al., Protein Eng (1999) 12: 439-446] crystal forms., pH 7.5, vapor diffusion, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2003 / Details: CONFOCAL OPTICS
RadiationMonochromator: CONFOCAL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 31105 / % possible obs: 96.2 % / Rmerge(I) obs: 0.075 / Χ2: 4.351 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.80.42829841.689192.1
2.8-2.910.35330791.971194
2.91-3.040.27430722.12195.6
3.04-3.20.21731072.449196.2
3.2-3.40.14431132.446196.3
3.4-3.660.09131412.396197.2
3.66-4.030.06131252.451197.4
4.03-4.610.04531642.483197.6
4.61-5.80.0431762.282198
5.8-300.031314423.183197.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
MERLOTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→28.163 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 1.97 / Phase error: 26.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 1399 5.01 %
Rwork0.1997 --
obs0.2019 27905 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.23 Å2 / Biso mean: 43.1098 Å2 / Biso min: 12.8 Å2
Refinement stepCycle: LAST / Resolution: 2.8→28.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9198 0 144 75 9417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039570
X-RAY DIFFRACTIONf_angle_d1.20712900
X-RAY DIFFRACTIONf_chiral_restr0.1211430
X-RAY DIFFRACTIONf_plane_restr0.0041656
X-RAY DIFFRACTIONf_dihedral_angle_d14.3463566
Refine LS restraints NCSNumber: 5405 / Type: POSITIONAL / Rms dev position: 12.635 Å
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.90.31441430.26792602274594
2.9-3.0160.32151320.2582634276696
3.016-3.15310.28251390.23962631277096
3.1531-3.31910.28851420.24092620276296
3.3191-3.52670.28351400.2142650279096
3.5267-3.79840.23221400.19072685282597
3.7984-4.17950.20541480.17322663281197
4.1795-4.78170.23651360.1672676281297
4.7817-6.01480.2171410.20412684282598
6.0148-28.16420.20851380.17682661279996

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