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- PDB-6mdq: Crystal structure of equine serum albumin in complex with testosterone -

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Basic information

Entry
Database: PDB / ID: 6mdq
TitleCrystal structure of equine serum albumin in complex with testosterone
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Albumin / Equine Serum Albumin / Testosterone / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
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
CITRATE ANION / TESTOSTERONE / Albumin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCzub, M.P. / Majorek, K.A. / Shabalin, I.G. / Handing, K.B. / Venkataramany, B.S. / Cymborowski, M.T. / Satchell, K.J. / Joachimiak, A. / 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: 2019
Title: Testosterone meets albumin - the molecular mechanism of sex hormone transport by serum albumins.
Authors: Czub, M.P. / Venkataramany, B.S. / Majorek, K.A. / Handing, K.B. / Porebski, P.J. / Beeram, S.R. / Suh, K. / Woolfork, A.G. / Hage, D.S. / Shabalin, I.G. / Minor, W.
History
DepositionSep 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / 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 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

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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)66,9126
Polymers65,7681
Non-polymers1,1445
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint3 kcal/mol
Surface area26120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.244, 94.244, 142.345
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 / Source: (natural) Equus caballus (horse) / References: UniProt: P35747
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-TES / TESTOSTERONE / Testosterone


Mass: 288.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H28O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsthis mutation is characteristic for Equus ferus przewalskii, a rare subspecies of wild horse from ...this mutation is characteristic for Equus ferus przewalskii, a rare subspecies of wild horse from central Asia. See NCBI database, accession code: XP_008524663.1

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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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 ul of 15 mg/ml protein was mixed with 0.2 ul of the well condition (1.8 M ammonium dihydrogen citrate, pH 7.0) and equilibrated against well solution in 96-Well sitting drop ...Details: 0.2 ul of 15 mg/ml protein was mixed with 0.2 ul of the well condition (1.8 M ammonium dihydrogen citrate, pH 7.0) and equilibrated against well solution in 96-Well sitting drop crystallization plate (Swissci). Testosterone powder was added to the crystallization drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2011 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 39149 / % possible obs: 99.7 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.028 / Rrim(I) all: 0.076 / Χ2: 0.981 / Net I/σ(I): 10 / Num. measured all: 298193
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.196.81.02719100.8110.4241.1120.764100
2.19-2.237.50.8719760.8960.3360.9330.775100
2.23-2.277.70.78219650.9190.2980.8370.807100
2.27-2.327.60.67719610.9340.2590.7250.785100
2.32-2.377.70.54819500.9580.2090.5870.778100
2.37-2.427.70.44419710.9670.1690.4750.772100
2.42-2.487.70.36419560.9780.1390.390.791100
2.48-2.557.70.29819580.9850.1140.3190.822100
2.55-2.627.70.24819550.990.0950.2660.857100
2.62-2.717.70.20319510.9910.0780.2180.894100
2.71-2.817.70.16619470.9930.0640.1780.905100
2.81-2.927.70.13619590.9940.0520.1450.972100
2.92-3.057.70.10119830.9960.0390.1081.12100
3.05-3.217.70.07719330.9970.030.0831.232100
3.21-3.417.70.06319790.9980.0240.0681.211100
3.41-3.687.70.05419600.9980.0210.0581.19100
3.68-4.057.70.04819600.9980.0190.0521.262100
4.05-4.637.60.04619870.9980.0180.0491.27799.8
4.63-5.837.60.04219650.9990.0160.0451.12399.7
5.83-507.20.03419230.9990.0140.0371.27695.3

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Processing

Software
NameVersionClassification
HKL-3000data reduction
SCALEPACKdata scaling
HKL-3000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V08

3v08


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 12.041 / SU ML: 0.15 / SU R Cruickshank DPI: 0.2083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.178
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 1859 4.8 %RANDOM
Rwork0.1833 ---
obs0.1853 36951 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 209.58 Å2 / Biso mean: 64.487 Å2 / Biso min: 34.79 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å21.09 Å20 Å2
2--2.18 Å2-0 Å2
3----7.07 Å2
Refinement stepCycle: final / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4475 0 81 214 4770
Biso mean--105.94 60.74 -
Num. residues----580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194703
X-RAY DIFFRACTIONr_bond_other_d0.0010.024242
X-RAY DIFFRACTIONr_angle_refined_deg0.8211.9726405
X-RAY DIFFRACTIONr_angle_other_deg0.739904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9975587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40524.928207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23615780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3611519
X-RAY DIFFRACTIONr_chiral_restr0.0440.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215227
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02896
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 131 -
Rwork0.288 2744 -
all-2875 -
obs--100 %
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)
12.94461.61360.58037.22441.32362.204-0.0253-0.06760.336-0.45110.08030.3159-0.24790.0424-0.05510.2118-0.10990.01540.1344-0.00540.360347.8141.99973.463
25.93750.76820.87834.77042.51845.35540.18040.03280.094-0.51060.01950.0324-0.7416-0.3688-0.19980.3167-0.03220.03550.24160.1010.441933.69843.25971.539
34.3151-3.7552-8.293713.305111.841525.58810.07480.45740.2421-1.2166-0.11750.46-0.3601-0.10970.04280.3986-0.1522-0.25730.27040.10360.40435.87628.02562.555
46.01181.0675-2.09463.8845-0.30315.6697-0.31960.3544-0.1638-1.25460.2505-0.73620.02120.87750.06920.5357-0.17730.2020.2899-0.05020.455255.54827.34261.876
51.43850.55280.83333.75690.23562.80770.0332-0.01150.0447-0.00950.0021-0.2710.01510.4762-0.03520.0362-0.0377-0.01340.1419-0.02960.29347.74419.01382.586
62.99930.5468-1.43242.1143-0.85215.56310.0231-0.3598-0.05790.3487-0.05490.20340.0179-0.16880.03190.19080.0067-0.01980.0703-0.0020.304133.0762.01794.23
72.0312-0.45770.3262.10110.77523.2486-0.0006-0.0413-0.0209-0.1539-0.03230.04250.21490.01450.0330.1309-0.0224-0.0220.0132-0.0130.272333.8635.56366.087
82.26230.2229-1.32011.83270.11085.23850.2380.16520.0215-0.6145-0.2166-0.0385-0.1505-0.1709-0.02130.41710.1091-0.03990.044-0.01260.303733.5552.93343.265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 59
2X-RAY DIFFRACTION2A60 - 101
3X-RAY DIFFRACTION3A102 - 115
4X-RAY DIFFRACTION4A116 - 175
5X-RAY DIFFRACTION5A176 - 300
6X-RAY DIFFRACTION6A301 - 386
7X-RAY DIFFRACTION7A387 - 497
8X-RAY DIFFRACTION8A498 - 583

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