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Basic information

Entry
Database: PDB / ID: 4emx
TitleCrystal structure analysis of Human Serum Albumin in complex with chloride anions at cryogenic temperature
ComponentsSerum albumin
KeywordsPROTEIN 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


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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBotti, H. / Bonilla, L. / Trajtenberg, F. / Radi, R. / Buschiazzo, A.
CitationJournal: to be published
Title: New insights on B factors in crystal structure analysis and crystallographic model refinement
Authors: Botti, H. / Bonilla, L. / Trajtenberg, F. / Radi, R. / Buschiazzo, A.
History
DepositionApr 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,3558
Polymers133,1422
Non-polymers2136
Water4,107228
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6784
Polymers66,5711
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6784
Polymers66,5711
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.880, 59.230, 95.610
Angle α, β, γ (deg.)75.170, 87.830, 74.200
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLYSLYS4AA4 - 1994 - 199
21LYSLYSLYSLYS4BB4 - 1994 - 199
12CYSCYSLYSLYS3AA200 - 389200 - 389
22CYSCYSLYSLYS3BB200 - 389200 - 389
13GLNGLNALAALA1AA390 - 582390 - 582
23GLNGLNALAALA1BB390 - 582390 - 582

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Serum albumin


Mass: 66571.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2009 / Details: Crystal Type: Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 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) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.28-2.42.60.3671.91977675790.36795
2.4-2.552.60.2342.91875372100.23495
2.55-2.732.60.1631.21757867320.16394.7
2.73-2.942.60.1076.41644863080.10795
2.94-3.222.60.0788.31495457220.07894.3
3.22-3.612.60.0629.51343551580.06293.9
3.61-4.162.60.0569.31182345120.05692.3
4.16-5.12.60.0511.7929436240.0588.9
5.1-7.212.70.05411.1792028830.05490.6
7.21-25.7232.70.04114.8340112450.04172

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 1010 2 %RANDOM
Rwork0.1873 ---
obs0.1883 49673 93.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 185.73 Å2 / Biso mean: 76.1408 Å2 / Biso min: 16.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0.17 Å2-0.76 Å2
2---0.19 Å21.43 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9079 0 6 228 9313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.029362
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9712685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95551176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09624.744430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.462151670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9731549
X-RAY DIFFRACTIONr_chiral_restr0.1110.21415
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217040
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11539MEDIUM POSITIONAL0.240.5
11539MEDIUM THERMAL5.312
2693LOOSE POSITIONAL0.075
2745TIGHT THERMAL2.890.5
2693LOOSE THERMAL3.9510
31451TIGHT THERMAL4.610.5
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 79 -
Rwork0.245 3678 -
all-3757 -
obs--94.73 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.47280.08230.33522.3702-0.01773.66960.1635-0.06480.06620.10590.01580.12420.2803-0.6936-0.17930.0983-0.0726-0.01840.1380.03780.0789-8.5357-15.8473-2.8526
21.811.14510.69474.9701-0.58972.2367-0.12260.11570.11510.1335-0.2528-1.3-0.18570.36790.37540.0643-0.0127-0.07750.0810.11630.630819.49090.7674-4.65
34.0880.062-0.64172.72-0.26683.68490.1012-0.42050.3370.85970.1040.2351-0.6212-0.4977-0.20530.53620.07790.11910.16710.07160.2704-9.525915.63357.049
41.18590.5190.9451.35921.20975.00670.1682-0.1513-0.32260.115-0.0519-0.02560.6696-0.6378-0.11630.1081-0.0304-0.02680.39420.06520.1556-22.6481-25.1137-42.9529
52.78380.5453-0.17961.7018-0.73492.55730.00730.10390.26550.0506-0.2614-0.2595-0.42770.3060.25410.11580.03130.00320.31510.17470.16050.7166-2.3891-42.0686
62.15140.97520.07932.97110.82174.61780.02250.3898-0.3459-0.30050.0187-0.39180.68960.1817-0.04120.21390.1082-0.01640.55370.06910.25837.242-34.4656-52.5555
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 199
2X-RAY DIFFRACTION2A200 - 389
3X-RAY DIFFRACTION3A390 - 582
4X-RAY DIFFRACTION4B2 - 199
5X-RAY DIFFRACTION5B200 - 389
6X-RAY DIFFRACTION6B390 - 582

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