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- PDB-1e7a: Crystal structure of human serum albumin complexed with the gener... -

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Basic information

Entry
Database: PDB / ID: 1e7a
TitleCrystal structure of human serum albumin complexed with the general anesthetic propofol
ComponentsSERUM ALBUMIN
KeywordsCARRIER PROTEIN / ALBUMIN / GENERAL ANESTHETIC / PROPOFOL
Function / homology
Function and homology information


exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / 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
2,6-BIS(1-METHYLETHYL)PHENOL / Albumin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBhattacharya, A.A. / Curry, S. / Franks, N.P.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Binding of the General Anesthetics Propofol and Halothane to Human Serum Albumin. High Resolution Crystal Structures
Authors: Bhattacharya, A.A. / Curry, S. / Franks, N.P.
History
DepositionAug 26, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERUM ALBUMIN
B: SERUM ALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,8566
Polymers133,1422
Non-polymers7134
Water2,162120
1
A: SERUM ALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9283
Polymers66,5711
Non-polymers3572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SERUM ALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9283
Polymers66,5711
Non-polymers3572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.400, 55.610, 120.500
Angle α, β, γ (deg.)81.11, 90.57, 65.50
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.4241, 0.9054, 0.0224), (0.9055, -0.4243, 0.0088), (0.0175, 0.0165, -0.9997)
Vector: -47.9837, -34.0291, 58.0861)

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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) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P02768
#2: Chemical
ChemComp-PFL / 2,6-BIS(1-METHYLETHYL)PHENOL / 2,6-DIISOPROPYLPHENOL / PROPOFOL


Mass: 178.271 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H18O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSERUM ALBUMIN, REGULATES THE COLLOIDAL OSMOTIC PRESSURE OF BLOOD IT BINDS TO WATER, CA++, NA+, K+, ...SERUM ALBUMIN, REGULATES THE COLLOIDAL OSMOTIC PRESSURE OF BLOOD IT BINDS TO WATER, CA++, NA+, K+, FATTY ACIDS, HORMONES, BILIRUBIN AND DRUGS
Sequence detailsRESIDUES 1-24 IN P02768 ENTRY ARE SIGNAL SEQUENCE. RESIDUE 1 IN STRUCTURE COORDINATES IS EQUIVALENT ...RESIDUES 1-24 IN P02768 ENTRY ARE SIGNAL SEQUENCE. RESIDUE 1 IN STRUCTURE COORDINATES IS EQUIVALENT OF RESIDUE 25 IN P02768.

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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: 50.76 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
128-30 %(w/v)PEG33501reservoir
250 mMpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Oct 15, 1999 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→29.88 Å / Num. obs: 62870 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 7.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.296 / % possible all: 93.4
Reflection shell
*PLUS
% possible obs: 93.4 %

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AO6

1ao6


Resolution: 2.2→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED REFINEMENT WAS PERFORMED WITH MAX ALLOWABLE TEMPERATURE FACTOR OF 150
RfactorNum. reflection% reflectionSelection details
Rfree0.272 3143 5 %RANDOM
Rwork0.248 ---
obs0.248 62859 96.1 %-
Displacement parametersBiso mean: 59.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.35 Å
Luzzati d res low-20 Å
Luzzati sigma a0.41 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8950 0 52 120 9122
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.86
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.221.5
X-RAY DIFFRACTIONx_mcangle_it2.182
X-RAY DIFFRACTIONx_scbond_it1.882
X-RAY DIFFRACTIONx_scangle_it3.122.5
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.353 386 5.1 %
Rwork0.35 7223 -
obs--92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PFL.PARTOPH19.SOL
X-RAY DIFFRACTION3PFL.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.86
LS refinement shell
*PLUS
Rfactor Rwork: 0.35

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