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- PDB-4jk4: Crystal Structure of Bovine Serum Albumin in complex with 3,5-dii... -

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Basic information

Entry
Database: PDB / ID: 4jk4
TitleCrystal Structure of Bovine Serum Albumin in complex with 3,5-diiodosalicylic acid
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Bovine Serum Albumin / Helical protein possessing three domains / Transport / Fatty acids / hormones / metabolites and drugs / Plasma
Function / homology
Function and homology information


cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / protein-containing complex / DNA binding / extracellular space ...cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / protein-containing complex / DNA binding / extracellular space / extracellular region / metal ion binding / 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
2-HYDROXY-3,5-DIIODO-BENZOIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Albumin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.653 Å
AuthorsZielinski, K. / Bujacz, A. / Sekula, B. / Bujacz, G.
CitationJournal: Int.J.Biol.Macromol. / Year: 2013
Title: Crystallographic studies of the complexes of bovine and equine serum albumin with 3,5-diiodosalicylic acid.
Authors: Sekula, B. / Zielinski, K. / Bujacz, A.
History
DepositionMar 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)137,75124
Polymers133,1242
Non-polymers4,62722
Water2,612145
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,01513
Polymers66,5621
Non-polymers2,45312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,73611
Polymers66,5621
Non-polymers2,17410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)215.410, 44.800, 146.900
Angle α, β, γ (deg.)90.00, 115.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Serum albumin / BSA


Mass: 66561.969 Da / Num. of mol.: 2 / Fragment: UNP residues 25-607 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02769

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Non-polymers , 6 types, 167 molecules

#2: Chemical
ChemComp-DIU / 2-HYDROXY-3,5-DIIODO-BENZOIC ACID / 2-HYDROXY-3,5-DIIODOBENZOIC ACID


Mass: 389.914 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H4I2O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% MMEPEG 5000, 0.2M Calcium acetate, 0.1M MES 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2012 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 37411 / Num. obs: 36876 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 60.82 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.082 / Net I/σ(I): 14.47
Reflection shellResolution: 2.65→2.75 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 2.56 / Num. unique all: 3852 / Rsym value: 0.826 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F5S

4f5s


Resolution: 2.653→36.528 Å / SU ML: 0.36 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 1840 5 %random
Rwork0.1876 ---
all0.1906 37411 --
obs0.1906 36804 98.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.03 Å2
Refinement stepCycle: LAST / Resolution: 2.653→36.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9290 0 185 145 9620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.029711
X-RAY DIFFRACTIONf_angle_d1.95113046
X-RAY DIFFRACTIONf_dihedral_angle_d18.3753697
X-RAY DIFFRACTIONf_chiral_restr0.1081425
X-RAY DIFFRACTIONf_plane_restr0.011686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6534-2.72510.34671400.29172644X-RAY DIFFRACTION99
2.7251-2.80530.34361430.29362706X-RAY DIFFRACTION99
2.8053-2.89580.35381380.26012657X-RAY DIFFRACTION99
2.8958-2.99930.34041430.24242713X-RAY DIFFRACTION100
2.9993-3.11930.34591410.23172661X-RAY DIFFRACTION100
3.1193-3.26120.34881420.22142725X-RAY DIFFRACTION100
3.2612-3.4330.27711450.21192743X-RAY DIFFRACTION100
3.433-3.64790.28221390.192649X-RAY DIFFRACTION100
3.6479-3.92920.22511420.17022699X-RAY DIFFRACTION99
3.9292-4.32410.21711410.16112670X-RAY DIFFRACTION98
4.3241-4.94850.20341430.15182716X-RAY DIFFRACTION98
4.9485-6.22950.21331420.18322700X-RAY DIFFRACTION98
6.2295-36.5310.19341410.16422681X-RAY DIFFRACTION93
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)
10.66740.58480.52581.3976-0.24181.52840.0126-0.09030.0695-0.3275-0.0730.3476-0.1354-0.21780.04410.31150.0254-0.03050.14480.00190.184174.797827.06293.9993
21.9071.1954-0.45142.382-0.54661.05080.1885-0.3190.26070.3427-0.09391.0704-0.1865-0.5895-0.04430.3233-0.18340.02970.37040.04850.269871.683818.240322.8987
30.81790.4215-0.41060.9755-0.76921.39020.5084-0.0485-0.79210.2201-0.60040.40720.185-0.3499-0.01550.2878-0.33360.2036-0.01070.3254-0.056780.853712.885725.113
41.4584-0.38330.29980.49710.00780.50790.0424-0.16350.2044-0.3809-0.0054-0.2087-0.21680.0683-0.03790.2498-0.02960.0580.2134-0.02770.147299.309323.610411.6825
52.3346-0.22030.34291.11410.0651.3980.1476-0.2647-0.4748-0.08820.008-0.05810.37710.0141-0.13650.3725-0.0469-0.04660.19490.06440.228496.50829.013311.6464
62.04261.4838-0.62171.8423-0.0851.31810.0244-0.1339-0.1628-0.57780.1396-0.3020.15430.3547-0.01210.21220.02580.01890.3739-0.04020.3373119.401524.183714.7325
72.63691.3598-0.84472.3018-0.71861.43860.1617-0.22820.21030.58840.2949-0.2959-0.37010.2764-0.14850.137-0.03920.04020.339-0.1460.3672116.260932.485120.7527
83.95790.8131-3.19830.3674-0.82072.62270.1091-0.6822-0.08720.66180.1126-0.5369-0.12530.5243-0.13080.2759-0.0318-0.10020.5989-0.07280.3823110.672928.274635.4725
91.75120.349-0.24653.0326-1.03112.2212-0.4426-0.4852-0.27210.05420.2135-0.29450.26190.25660.0169-0.28530.47091.31240.3242-0.5505-1.542391.049535.212742.0357
101.5155-0.2205-0.20391.51620.16571.2964-0.1484-0.0045-0.41870.18260.09410.19230.15650.21290.05010.25210.01690.07470.33050.00220.228892.933128.491532.4605
111.7611-0.4384-0.23660.6154-0.37790.42630.1328-0.03580.36850.16520.286-0.4727-0.67770.4879-0.18820.2815-0.02090.05090.2532-0.06030.327298.00942.284232.0508
122.2754-0.0853-0.211.87690.29531.7621-0.7427-0.5950.2555-0.11760.26910.20250.3054-0.46440.04660.2931-0.06290.26290.35410.08060.133378.150237.64546.354
132.351-0.77-0.49691.32280.01541.8852-0.1786-0.3959-0.43030.16860.24960.1553-0.02260.0743-0.09640.57180.30690.08180.68490.08350.39877.260335.933657.3669
140.48730.75620.42612.0967-0.17431.6792-0.02430.0262-0.0413-0.58170.0731-0.15140.24240.2624-0.0460.3817-0.0304-0.05720.1497-0.04450.22938.729518.801317.1143
151.45440.7161-0.46422.9894-0.80351.39120.11440.185-0.1760.4957-0.0418-0.7868-0.27770.67650.02090.2208-0.1262-0.02850.39340.02980.332251.821327.834731.0645
161.75410.73330.5431.55240.12031.3736-0.2232-0.32070.24260.2618-0.2348-0.0883-0.60580.50060.0820.3375-0.2149-0.08580.2447-0.01210.312145.65833.240137.9852
171.2116-0.1361-0.54420.7349-0.03871.08210.0084-0.2885-0.3518-0.1531-0.05410.2453-0.0897-0.1671-0.04970.2380.0486-0.06280.2408-0.00070.246822.916722.37737.6577
181.851-0.0341-0.52821.59290.40012.1542-0.0844-0.20710.36920.33590.19660.0246-0.6935-0.0567-0.10980.47770.0468-0.02220.1956-0.00090.272525.285837.041135.8284
192.31490.6402-0.37082.2159-0.37761.95250.3468-0.2951-0.26670.30640.12010.82870.0766-0.6429-0.08930.37590.0120.08120.57510.08410.67477.612422.0851.0212
201.4942-0.7187-0.92580.7585-0.2531.76490.3402-0.3933-0.55290.01720.37980.36760.8053-0.3133-0.19220.3611-0.1821-0.06230.7420.34040.8713.15614.142354.6904
213.44020.55080.29310.2080.02640.1018-0.223-0.15010.10580.72680.29470.10580.0614-0.1915-0.13921.05110.12350.17540.84380.03590.425726.078917.932463.7764
221.7148-0.604-0.04922.7211.32862.6203-0.1113-0.42540.4074-0.1113-0.038-0.32920.0758-0.0239-0.00190.35940.2023-0.1190.35350.01290.529447.110910.96357.8974
232.51440.23590.2972.60630.08312.0727-0.2153-0.11460.46460.24290.1797-0.0465-0.14940.05370.02910.14150.0215-0.08510.31420.0250.296739.820317.587751.1924
240.37930.0968-0.27490.11280.02070.3063-0.1942-0.5763-0.53890.5958-0.46820.36380.5248-0.40490.11960.52790.0768-0.0930.37640.35090.859235.71713.834753.6554
252.08840.332-0.46411.85480.0341.0443-0.0326-0.16580.2411-0.1403-0.0350.10030.06530.33880.01510.19910.0269-0.06330.46040.05820.606760.14748.630253.301
262.5373-0.5231-0.24792.2820.43031.9842-0.1566-0.11980.28310.41430.2138-0.1276-0.25630.16640.00580.32650.1244-0.03770.5262-0.09460.295767.72329.949461.1256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 2:106)
2X-RAY DIFFRACTION2(chain A and resseq 107:147)
3X-RAY DIFFRACTION3(chain A and resseq 148:198)
4X-RAY DIFFRACTION4(chain A and resseq 199:250)
5X-RAY DIFFRACTION5(chain A and resseq 251:295)
6X-RAY DIFFRACTION6(chain A and resseq 296:336)
7X-RAY DIFFRACTION7(chain A and resseq 337:366)
8X-RAY DIFFRACTION8(chain A and resseq 367:398)
9X-RAY DIFFRACTION9(chain A and resseq 399:417)
10X-RAY DIFFRACTION10(chain A and resseq 418:468)
11X-RAY DIFFRACTION11(chain A and resseq 469:497)
12X-RAY DIFFRACTION12(chain A and resseq 498:537)
13X-RAY DIFFRACTION13(chain A and resseq 538:583)
14X-RAY DIFFRACTION14(chain B and resseq 2:106)
15X-RAY DIFFRACTION15(chain B and resseq 107:147)
16X-RAY DIFFRACTION16(chain B and resseq 148:198)
17X-RAY DIFFRACTION17(chain B and resseq 199:250)
18X-RAY DIFFRACTION18(chain B and resseq 251:295)
19X-RAY DIFFRACTION19(chain B and resseq 296:336)
20X-RAY DIFFRACTION20(chain B and resseq 337:366)
21X-RAY DIFFRACTION21(chain B and resseq 367:398)
22X-RAY DIFFRACTION22(chain B and resseq 399:417)
23X-RAY DIFFRACTION23(chain B and resseq 418:468)
24X-RAY DIFFRACTION24(chain B and resseq 469:497)
25X-RAY DIFFRACTION25(chain B and resseq 498:537)
26X-RAY DIFFRACTION26(chain B and resseq 538:583)

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