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- PDB-7mbl: Crystal structure of Equine Serum Albumin in complex with Cobalt (II) -

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Basic information

Entry
Database: PDB / ID: 7mbl
TitleCrystal structure of Equine Serum Albumin in complex with Cobalt (II)
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / serum albumin / complex with Cobalt / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsShabalin, I.G. / Czub, M.P. / Handing, K.B. / Cymborowski, M.T. / Grabowski, M. / Cooper, D.R. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Chem Sci / Year: 2023
Title: Structural and biochemical characterisation of Co 2+ -binding sites on serum albumins and their interplay with fatty acids.
Authors: Wu, D. / Gucwa, M. / Czub, M.P. / Cooper, D.R. / Shabalin, I.G. / Fritzen, R. / Arya, S. / Schwarz-Linek, U. / Blindauer, C.A. / Minor, W. / Stewart, A.J.
History
DepositionMar 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)66,44710
Polymers65,7681
Non-polymers6799
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-94 kcal/mol
Surface area27040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.312, 93.312, 141.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Serum albumin


Mass: 65768.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: isolated from blood of common horse (Equus caballus)
Source: (natural) Equus caballus (horse) / Tissue: blood / References: UniProt: P35747
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 291 K / Method: counter-diffusion / pH: 7.4
Details: Protein: 1 uL of 34 mg/mL ESA dissolved in 10 mM Tris (pH 7.4) and 150 mM NaCl. Precipitant: 1 uL of 0.2 M lithium sulfate, 2.0 M ammonium sulfate, 0.1 M Tris pH 7.4. 15-Well hanging drop ...Details: Protein: 1 uL of 34 mg/mL ESA dissolved in 10 mM Tris (pH 7.4) and 150 mM NaCl. Precipitant: 1 uL of 0.2 M lithium sulfate, 2.0 M ammonium sulfate, 0.1 M Tris pH 7.4. 15-Well hanging drop crystallization plate (Qiagen, EasyXtal). 3.3 uL of 50 mM cobalt (II) chloride dissolved in the reservoir solution were added directly to the 2 uL crystallization drop containing crystals to reach a final cobalt concentration of 31 mM and then incubated for a few hours before harvesting. Paratone was used as a cryoprotectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2017
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal monochromator: water cooled;
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 19239 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 54.2 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.044 / Rrim(I) all: 0.099 / Rsym value: 0.089 / Χ2: 0.854 / Net I/av σ(I): 17.28 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allRsym valueΧ2% possible all
2.7-2.755.11.1241.39820.7510.9260.5571.2561.1240.802100
2.75-2.85.10.8659160.7980.4260.9650.816100
2.8-2.855.10.7329780.8060.3620.8180.793100
2.85-2.915.10.629620.8640.3060.6920.766100
2.91-2.975.10.5139570.9180.2530.5720.89100
2.97-3.0450.4279550.8850.2140.4791.399100
3.04-3.1250.3899690.9430.1940.4361.014100
3.12-3.25.10.289520.9040.140.3131.161100
3.2-3.35.10.229540.9750.1090.2460.769100
3.3-3.45.10.1449460.9890.0710.1610.739100
3.4-3.525.10.1329730.980.0650.1480.771100
3.52-3.665.10.0989540.9920.0490.110.725100
3.66-3.835.10.0889620.9940.0430.0980.821100
3.83-4.035.10.0789720.9940.0390.0870.877100
4.03-4.295.10.0549520.9960.0270.0610.719100
4.29-4.6250.0599630.9960.0290.0661.117100
4.62-5.0850.0399600.9980.0190.0440.622100
5.08-5.8150.0459830.9980.0220.0510.65100
5.81-7.3250.0359690.9980.0180.040.572100
7.32-504.60.0279800.9980.0140.0311.09998.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
HKL-3000data collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IIU

5iiu


Resolution: 2.7→46.7 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.877 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.1802 / FOM work R set: 0.7456 / SU B: 35.506 / SU ML: 0.335 / SU Rfree: 0.4264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2892 928 5.2 %RANDOM
Rwork0.2133 ---
obs0.2174 16913 92.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.97 Å2 / Biso mean: 58.041 Å2 / Biso min: 16.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.11 Å2-0 Å2
2---0.23 Å20 Å2
3---0.74 Å2
Refinement stepCycle: final / Resolution: 2.7→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4582 0 25 67 4674
Biso mean--94.83 61.37 -
Num. residues----581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134742
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174412
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.656375
X-RAY DIFFRACTIONr_angle_other_deg1.151.58510277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9475580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02723.691233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2615851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9111520
X-RAY DIFFRACTIONr_chiral_restr0.0580.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025228
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02973
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 29 -
Rwork0.281 682 -
all-711 -
obs--49.96 %
Refinement TLS params.Method: refined / Origin x: 40.105 Å / Origin y: 16.756 Å / Origin z: 70.759 Å
111213212223313233
T0.1476 Å2-0.0874 Å2-0.0308 Å2-0.1664 Å20.0394 Å2--0.0287 Å2
L0.3947 °2-0.0359 °20.3778 °2-1.3317 °20.6864 °2--1.8729 °2
S-0.0382 Å °0.0609 Å °0.0427 Å °-0.1126 Å °0.0083 Å °-0.1297 Å °-0.1661 Å °0.351 Å °0.0299 Å °

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