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- PDB-1bm0: CRYSTAL STRUCTURE OF HUMAN SERUM ALBUMIN -

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Basic information

Entry
Database: PDB / ID: 1bm0
TitleCRYSTAL STRUCTURE OF HUMAN SERUM ALBUMIN
ComponentsSERUM ALBUMIN
KeywordsCARRIER PROTEIN / ALBUMIN
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSugio, S. / Kashima, A. / Mochizuki, S. / Noda, M. / Kobayashi, K.
Citation
Journal: Protein Eng. / Year: 1999
Title: Crystal structure of human serum albumin at 2.5 A resolution.
Authors: Sugio, S. / Kashima, A. / Mochizuki, S. / Noda, M. / Kobayashi, K.
#1: Journal: Adv.Protein Chem. / Year: 1994
Title: Structure of Serum Albumin
Authors: Carter, D.C. / Ho, J.X.
#2: 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.
#3: Journal: Nature / Year: 1993
Title: Erratum. Atomic Structure and Chemistry of Human Serum Albumin
Authors: He, X.M. / Carter, D.C.
#4: Journal: Nature / Year: 1992
Title: Atomic Structure and Chemistry of Human Serum Albumin
Authors: He, X.M. / Carter, D.C.
#5: Journal: Science / Year: 1990
Title: Structure of Human Serum Albumin
Authors: Carter, D.C. / He, X.M.
#6: 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
DepositionJul 28, 1998Processing site: BNL
Revision 1.0Jul 28, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Water724
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
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
Unit cell
Length a, b, c (Å)59.360, 96.890, 59.240
Angle α, β, γ (deg.)91.04, 103.40, 74.94
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) / Tissue: PLASMA / Production host: Pichia pastoris (fungus) / References: UniProt: P02768
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Density % sol: 77 %
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop / PH range low: 5.5 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1150-255 mg/mlprotein1drop
250 mMpotassium phosphate1drop
330-38 %(v/v)PEG4001drop
45 mMsodium azide1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 14, 1996 / Details: YALE/MSC MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.37→93.47 Å / Num. obs: 36149 / % possible obs: 71.3 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 4.37
Reflection shellResolution: 2.37→2.5 Å / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 1.52 / % possible all: 36.1
Reflection shell
*PLUS
% possible obs: 36 %

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Processing

Software
NameClassification
CONTROLdata collection
PROCESSdata reduction
X-PLORmodel building
X-PLORrefinement
CONTROLdata reduction
PROCESSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN SERUM ALBUMIN (1AO6)

1ao6


Resolution: 2.5→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: POSTERIORI / σ(F): 0
Details: THE AUTHORS USED BULK SOLVENT CORRECTION AND WEIGHTING SCHEME DEPENDENT ON RESOLUTIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.292 3337 10.1 %RANDOM
Rwork0.207 ---
obs0.207 33040 77.1 %-
Displacement parametersBiso mean: 40.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9200 0 0 4 9204
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_deg1.75
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.69
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
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.42 213 10.3 %
Rwork0.292 1863 -
obs--48.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.69
LS refinement shell
*PLUS
Rfactor Rfree: 0.42 / Rfactor obs: 0.292

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