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- PDB-4j2v: Crystal Structure of Equine Serum Albumin in complex with 3,5-dii... -

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Basic information

Entry
Database: PDB / ID: 4j2v
TitleCrystal Structure of Equine Serum Albumin in complex with 3,5-diiodosalicylic acid
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Equine serum albumin / Helical / Serum Albumin Superfamily / Transport / Fatty acids / 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 / 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
ACETATE ION / 2-HYDROXY-3,5-DIIODO-BENZOIC ACID / FORMIC ACID / MALONATE ION / Albumin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsSekula, B. / Bujacz, A. / Zielinski, K. / 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
DepositionFeb 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification ..._diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name / _software.version
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,55521
Polymers65,8541
Non-polymers2,70120
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.880, 88.880, 134.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serum albumin /


Mass: 65854.203 Da / Num. of mol.: 1 / Fragment: UNP residues 25-607 / Source method: isolated from a natural source / Details: Plasma / Source: (natural) Equus caballus (horse) / References: UniProt: P35747

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Non-polymers , 5 types, 251 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.: 4 / Source method: obtained synthetically / Formula: C7H4I2O3
#3: Chemical
ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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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: 47.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 85% Tacsimate, cocrystallization with 3,5-diiodosalicylic acid, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.932 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 21, 2011 / Details: Mirrors
RadiationMonochromator: Double crystal monochromator Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 2.12→33.39 Å / Num. all: 34046 / Num. obs: 34024 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.75 % / Biso Wilson estimate: 43.317 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.67
Reflection shellResolution: 2.12→2.22 Å / Redundancy: 5.74 % / Rmerge(I) obs: 0.925 / Mean I/σ(I) obs: 2.48 / Num. unique all: 4379 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
REFMAC(rigid body refinement)refinement
XDSdata scaling
XDSdata reduction
REFMAC(rigid body refinement)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F5U

4f5u


Resolution: 2.12→33.39 Å / SU ML: 0.3 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 1077 3.17 %random
Rwork0.1814 ---
all0.1832 34046 --
obs0.1832 34019 99.95 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.67 Å2
Refinement stepCycle: LAST / Resolution: 2.12→33.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4594 0 125 231 4950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.024858
X-RAY DIFFRACTIONf_angle_d1.8636520
X-RAY DIFFRACTIONf_dihedral_angle_d17.1361831
X-RAY DIFFRACTIONf_chiral_restr0.095703
X-RAY DIFFRACTIONf_plane_restr0.008859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1201-2.21660.36291230.27754091X-RAY DIFFRACTION100
2.2166-2.33340.34031300.25774146X-RAY DIFFRACTION100
2.3334-2.47960.30141270.2374103X-RAY DIFFRACTION100
2.4796-2.6710.2921440.22754080X-RAY DIFFRACTION100
2.671-2.93960.23951380.20024105X-RAY DIFFRACTION100
2.9396-3.36460.2431410.17544120X-RAY DIFFRACTION100
3.3646-4.23770.20841430.14424138X-RAY DIFFRACTION100
4.2377-33.39730.19991310.15724159X-RAY DIFFRACTION100
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)
15.7596-0.391-0.52584.1619-0.5931.42630.22960.05080.25770.34380.0844-0.1429-0.35540.0472-0.28050.48430.1173-0.00140.3051-0.02010.27-38.44839.937221.4436
28.83541.102-2.49912.46540.46493.723-0.0441-0.5120.28060.99980.15860.3431-0.0633-0.284-0.11160.68180.19130.05270.35750.01540.3119-46.978227.56834.3241
36.3543-0.8938-2.02082.8338-0.06963.0147-0.2331-0.0281-0.47310.58210.14830.6017-0.1361-0.78490.11190.39260.10490.1090.41870.0430.3099-51.268420.065628.8762
42.42130.4055-0.15614.21770.0991.7522-0.10090.230.1347-0.0505-0.02250.0203-0.0697-0.01480.12350.23020.0223-0.02830.23030.02470.1515-38.163418.56858.6295
51.99541.10520.75668.43950.76912.172-0.06440.33380.1156-0.05760.06160.7477-0.0737-0.58520.02280.2540.1259-0.00170.55490.05180.2772-52.156619.41928.7713
69.0506-1.7988-2.96352.81511.53125.55750.09580.84280.4462-0.6387-0.0796-0.0727-0.2335-0.1796-0.01940.4009-0.0384-0.01150.28940.02710.2206-34.60394.671-4.044
77.6916-0.0716-5.48295.04790.46839.7219-0.19330.0149-0.2623-0.36470.0699-0.41690.10040.75220.06790.2853-0.0316-0.03770.25090.00580.1752-27.95692.11812.9611
82.68940.2557-2.56250.30320.36157.4136-0.4406-0.0267-0.52-0.1511-0.0261-0.17220.91170.37150.49860.4973-0.01870.09230.17580.01750.3225-33.1225-5.182914.0399
95.1730.21130.31761.0020.33152.07220.1920.2264-0.00170.1579-0.1914-0.06580.065-0.02710.01620.25650.0101-0.00390.13720.03260.1637-30.65583.110734.3988
101.46440.66731.52062.53981.56426.3562-0.0367-0.0333-0.09460.2186-0.04810.060.3306-0.24550.10690.18730.0470.01470.15050.00540.1665-35.80778.162526.4642
116.64361.23532.7224.25431.37795.73960.21470.33550.0033-0.027-0.1745-0.58560.64320.640.00140.21920.04360.03360.1970.03350.2605-22.00896.759124.4712
127.1123-1.3926-4.33063.44251.18767.74740.0508-0.22340.1640.8426-0.1656-0.1713-0.4283-0.03430.08870.507-0.041-0.04530.15190.05470.2117-30.85987.09746.647
135.2067-3.0196-0.76025.20192.26331.90490.214-0.2698-0.27190.5062-0.23950.09170.3129-0.02030.01920.5907-0.0593-0.07690.23290.06430.2845-32.8139-0.467752.5247
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 3:106)
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)

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