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- PDB-1uor: X-RAY STUDY OF RECOMBINANT HUMAN SERUM ALBUMIN. PHASES DETERMINED... -

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Basic information

Entry
Database: PDB / ID: 1uor
TitleX-RAY STUDY OF RECOMBINANT HUMAN SERUM ALBUMIN. PHASES DETERMINED BY MOLECULAR REPLACEMENT METHOD, USING LOW RESOLUTION STRUCTURE MODEL OF TETRAGONAL FORM OF HUMAN SERUM ALBUMIN
ComponentsSERUM ALBUMIN
KeywordsMETAL BINDING PROTEIN / PLASMA PROTEIN / METAL-BINDING 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 / cellular response to starvation / 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 / endoplasmic reticulum / Golgi apparatus / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCarter, D.C. / Ho, J.X.
Citation
Journal: Nature / Year: 1992
Title: Atomic structure and chemistry of human serum albumin.
Authors: He, X.M. / Carter, D.C.
#1: 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.
#2: Journal: Science / Year: 1990
Title: Structure of Human Serum Albumin
Authors: Carter, D.C. / He, X.M.
#3: 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
DepositionMar 10, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_keywords.text
Revision 1.4Nov 20, 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


Theoretical massNumber of molelcules
Total (without water)66,5711
Polymers66,5711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.860, 88.280, 60.680
Angle α, β, γ (deg.)90.00, 101.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SERUM ALBUMIN


Mass: 66571.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: 293 / Organ: PLASMA / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): 293 / References: UniProt: P02768
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: 2.32 Å3/Da / Density % sol: 49 %
Description: THE DATA IS 97. % COMPLETE TO 2.8 ANGSTROMS RESOLUTION.
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1120-180 mg/mlprotein1drop
240 %PEG4001drop
30.05 M1dropKH2PO4
40.05 M1reservoirKH2PO4
540 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.27→40 Å / Num. obs: 14772 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.08

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Processing

Software
NameClassification
R-AXISdata collection
R-AXISdata reduction
X-PLORmodel building
X-PLORrefinement
R-AXISdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN SERUM ALBUMIN (TETRAGONAL)

Resolution: 2.8→6 Å / Isotropic thermal model: YES / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.231 --
obs0.231 10672 97 %
Displacement parametersBiso mean: 23 Å2
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4617 0 0 0 4617
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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