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- PDB-4k2c: HSA Ligand Free -

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Basic information

Entry
Database: PDB / ID: 4k2c
TitleHSA Ligand Free
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Heart Shape
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 / 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: 3.23 Å
AuthorsWang, Y. / Luo, Z. / Shi, X. / Huang, M.
CitationJournal: J. Biol. Chem. / Year: 2013
Title: Structural mechanism of ring-opening reaction of glucose by human serum albumin.
Authors: Wang, Y. / Yu, H. / Shi, X. / Luo, Z. / Lin, D. / Huang, M.
History
DepositionApr 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Data collection / Database references
Category: citation / diffrn_radiation_wavelength / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_wavelength_list

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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


Theoretical massNumber of molelcules
Total (without water)133,1422
Polymers133,1422
Non-polymers00
Water0
1
A: Serum albumin


Theoretical massNumber of molelcules
Total (without water)66,5711
Polymers66,5711
Non-polymers00
Water0
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.410, 179.888, 57.459
Angle α, β, γ (deg.)90.00, 105.86, 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.: 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
Production host: Pichia pastoris (fungus) / References: UniProt: 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 25-30% PEG 3350, pH 7, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.04 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 3.03→50 Å / Num. obs: 18979
Reflection shellHighest resolution: 3.03 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.23→47.7 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.927 / SU B: 83.872 / SU ML: 0.548 / Cross valid method: THROUGHOUT / ESU R Free: 0.763 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26507 754 5.1 %RANDOM
Rwork0.21294 ---
obs0.21572 13898 79.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 105.526 Å2
Baniso -1Baniso -2Baniso -3
1--2.38 Å2-0 Å22.52 Å2
2---2.33 Å2-0 Å2
3---3.44 Å2
Refinement stepCycle: LAST / Resolution: 3.23→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9182 0 0 0 9182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199394
X-RAY DIFFRACTIONr_bond_other_d0.0010.028958
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.97112700
X-RAY DIFFRACTIONr_angle_other_deg0.8563.00720670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20751156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24924.887442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.61151710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6111548
X-RAY DIFFRACTIONr_chiral_restr0.0840.21408
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022034
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.23→3.314 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 68 -
Rwork0.279 1246 -
obs--97.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.22380.0121-0.11810.185-0.130.1650.00290.040.0302-0.00710.03680.0290.0042-0.0087-0.03970.0113-0.0096-0.0190.0628-0.00120.04858.2334-0.11545.2931
20.21380.0734-0.12220.2025-0.04250.1079-0.08270.0126-0.04180.00990.07110.0190.0080.01470.01160.0668-0.00550.02340.0754-0.01140.027910.4521-46.54996.054
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 582
2X-RAY DIFFRACTION2B4 - 582

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