- PDB-4emx: Crystal structure analysis of Human Serum Albumin in complex with... -
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Basic information
Entry
Database: PDB / ID: 4emx
Title
Crystal structure analysis of Human Serum Albumin in complex with chloride anions at cryogenic temperature
Components
Serum albumin
Keywords
PROTEIN BINDING / plasma / drug binding / antioxidant / allostery / redox biology / all alpha / disulfide bond stabilized / human plasma osmotic regulation / transport / extracellular space / free radicals
Function / homology
Function and homology information
cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / 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 / 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
Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2 microL 100 mg/mL protein in 50 mM disodium/monosodium phosphate buffer and 100 mM NaCl were mixed with 2 uL 25% PEG 3350, 50 mM disodium/monosodium phosphate buffer, 100 mM NaCl, pH 7.5, ...Details: 2 microL 100 mg/mL protein in 50 mM disodium/monosodium phosphate buffer and 100 mM NaCl were mixed with 2 uL 25% PEG 3350, 50 mM disodium/monosodium phosphate buffer, 100 mM NaCl, pH 7.5, vapor diffusion, hanging drop, temperature 293K
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.0809 Å / Relative weight: 1
Reflection
Resolution: 2.28→25.566 Å / Num. all: 50973 / Num. obs: 50973 / % possible obs: 93.1 % / Redundancy: 2.6 % / Rsym value: 0.066 / Net I/σ(I): 9.7
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.28-2.4
2.6
0.367
1.9
19776
7579
0.367
95
2.4-2.55
2.6
0.234
2.9
18753
7210
0.234
95
2.55-2.73
2.6
0.163
1.2
17578
6732
0.163
94.7
2.73-2.94
2.6
0.107
6.4
16448
6308
0.107
95
2.94-3.22
2.6
0.078
8.3
14954
5722
0.078
94.3
3.22-3.61
2.6
0.062
9.5
13435
5158
0.062
93.9
3.61-4.16
2.6
0.056
9.3
11823
4512
0.056
92.3
4.16-5.1
2.6
0.05
11.7
9294
3624
0.05
88.9
5.1-7.21
2.7
0.054
11.1
7920
2883
0.054
90.6
7.21-25.723
2.7
0.041
14.8
3401
1245
0.041
72
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Phasing
Phasing
Method: molecular replacement
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Processing
Software
Name
Version
Classification
NB
MOSFLM
datareduction
SCALA
3.3.9
datascaling
AMoRE
phasing
REFMAC
refinement
PDB_EXTRACT
3.11
dataextraction
HKL-2000
datacollection
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25.5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2593 / WRfactor Rwork: 0.2025 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8281 / SU B: 17.279 / SU ML: 0.204 / SU R Cruickshank DPI: 0.4073 / SU Rfree: 0.2479 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.407 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2381
1010
2 %
RANDOM
Rwork
0.1873
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obs
0.1883
49673
93.03 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
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