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- PDB-4luh: Complex of ovine serum albumin with 3,5-diiodosalicylic acid -

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Basic information

Entry
Database: PDB / ID: 4luh
TitleComplex of ovine serum albumin with 3,5-diiodosalicylic acid
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Helical structure / transport / Fatty acids / metabolites
Function / homology
Function and homology information


enterobactin binding / lipid binding / extracellular space / metal ion binding
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
Chem-2Q5 / ACETATE ION / 2-HYDROXY-3,5-DIIODO-BENZOIC ACID / FORMIC ACID / (2S)-2-hydroxybutanedioic acid / MALONATE ION / SUCCINIC ACID / Albumin
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBujacz, A. / Talaj, J.A. / Pietrzyk, A.J. / Bujacz, G.
CitationJournal: To be Published
Title: Crystal structure of ovine serum albumin and its complex with 3,5-diiodosalicylic acid
Authors: Bujacz, A. / Talaj, J.A. / Pietrzyk, A.J.
History
DepositionJul 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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)68,75816
Polymers66,4281
Non-polymers2,33015
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.530, 118.530, 120.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-739-

HOH

21A-887-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serum albumin /


Mass: 66427.820 Da / Num. of mol.: 1 / Fragment: Mature form of ovine serum albumin / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: P14639

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Non-polymers , 8 types, 225 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.: 2 / Source method: obtained synthetically / Formula: C7H4I2O3
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#8: Chemical ChemComp-2Q5 / (2R)-2-{[(2R)-2-{[(2S)-2-{[(2R)-2-hydroxypropyl]oxy}propyl]oxy}propyl]oxy}propan-1-ol


Mass: 250.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O5
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 3.68 Å3/Da / Density % sol: 66.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 70% Tacsimate, 4% PPG 400, pH 7.0, 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: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2013 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 50089 / Num. obs: 50067 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.44 % / Biso Wilson estimate: 44.44 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 2.96
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 7.55 % / Rmerge(I) obs: 0.0843 / Mean I/σ(I) obs: 2.96 / Num. unique all: 6156 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4LUF

4luf


Resolution: 2.2→47.22 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.706 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20887 1503 3 %RANDOM
Rwork0.17098 ---
all0.17212 50089 --
obs0.17212 48564 99.96 %-
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 mean: 44.437 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.52 Å2-0 Å2
2--0.52 Å2-0 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4645 0 129 210 4984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194884
X-RAY DIFFRACTIONr_angle_refined_deg2.171.9946592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7495584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0124.955224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.94215870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7961522
X-RAY DIFFRACTIONr_chiral_restr0.1340.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213676
X-RAY DIFFRACTIONr_mcbond_it2.9443.0062336
X-RAY DIFFRACTIONr_mcangle_it3.9654.4882915
X-RAY DIFFRACTIONr_scbond_it6.0143.7712548
X-RAY DIFFRACTIONr_long_range_B_refined11.03827.3087754
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 110 -
Rwork0.23 3547 -
obs-3547 99.97 %
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)
10.40370.1465-0.39070.7907-0.26030.40960.05540.0894-0.0045-0.1813-0.0423-0.0856-0.0334-0.0993-0.01310.12650.0260.02170.09780.03320.074463.3937-17.5901-6.6947
20.09610.06920.26040.28320.32570.80160.01840.02330.01850.1376-0.0024-0.01130.18010.0572-0.0160.12550.00950.00190.0668-0.00590.129867.5416-35.27494.1795
31.4877-0.5174-0.22550.34910.17640.1302-0.1357-0.13250.14370.19440.11970.03520.17080.06830.01610.24740.08550.03650.04270.02020.06268.6084-31.915714.2123
40.11390.15550.04320.29690.17981.06060.02080.03790.070.01260.04820.0095-0.0225-0.0495-0.0690.1139-0.00180.01860.04570.01710.135354.6164-11.361516.83
51.1119-0.16-1.01530.63710.62691.3366-0.0258-0.10110.17770.08570.1681-0.01970.12610.2404-0.14230.11040.0333-0.00630.0829-0.0080.112268.7547-12.412220.9664
62.39880.06040.44930.00510.05080.7335-0.0208-0.02170.0842-0.00440.0114-0.0077-0.0937-0.03310.00930.12910.0317-0.00170.05850.00410.101945.7855-2.862933.7954
71.2281-1.41020.36112.10870.12680.73260.0193-0.1061-0.0746-0.0169-0.00440.07770.0583-0.1866-0.01480.0834-0.01320.00670.1030.01060.109438.3974-9.726931.6417
81.7063-4.353-0.476211.70881.75210.616-0.0679-0.117-0.12130.31580.10010.26110.1378-0.1446-0.03230.0931-0.02210.04360.08340.03160.110240.9463-25.023135.8276
92.3464-0.80141.26590.87240.50772.1606-0.0397-0.0937-0.05660.08120.01310.04060.0726-0.10670.02660.0847-0.0715-0.01860.0813-0.01280.113840.6239-40.929220.9345
100.64190.14920.34710.20050.32520.7439-0.00110.0856-0.01670.04040.0861-0.06950.0250.0166-0.08510.1202-0.0148-0.01590.1162-0.02220.085447.9929-31.978420.0685
111.40691.01210.63871.45471.01570.79440.0571-0.03430.12130.0308-0.18220.208-0.0172-0.04540.12510.0656-0.0419-0.01790.1294-0.03570.112134.2134-28.75817.6874
120.1899-0.2447-0.06530.9360.65810.55550.07940.06750.10180.184-0.0471-0.15020.229-0.0159-0.03240.16660.00710.00360.1095-0.0020.108542.4145-51.827512.7607
132.2082-1.7886-1.47651.5021.48843.3081-0.1779-0.1312-0.0790.25850.10890.06910.49560.14810.06890.278-0.04910.01820.03880.00880.014940.9569-61.519716.6657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 106
2X-RAY DIFFRACTION2A107 - 147
3X-RAY DIFFRACTION3A148 - 198
4X-RAY DIFFRACTION4A199 - 250
5X-RAY DIFFRACTION5A251 - 295
6X-RAY DIFFRACTION6A296 - 336
7X-RAY DIFFRACTION7A337 - 366
8X-RAY DIFFRACTION8A367 - 398
9X-RAY DIFFRACTION9A399 - 417
10X-RAY DIFFRACTION10A418 - 468
11X-RAY DIFFRACTION11A469 - 497
12X-RAY DIFFRACTION12A498 - 537
13X-RAY DIFFRACTION13A538 - 583

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