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- PDB-5iih: Crystal structure of Equine Serum Albumin in the presence of 2.5 ... -

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Basic information

Entry
Database: PDB / ID: 5iih
TitleCrystal structure of Equine Serum Albumin in the presence of 2.5 mM zinc at pH 7.4
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / small molecule binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / blood microparticle / protein-containing complex ...cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / small molecule binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / blood microparticle / protein-containing complex / DNA binding / 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: 2.4 Å
AuthorsHanding, K.B. / Shabalin, I.G. / Cooper, D.R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM117325-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5U54GM094662-05 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM053163 United States
CitationJournal: Chem Sci / Year: 2016
Title: Circulatory zinc transport is controlled by distinct interdomain sites on mammalian albumins.
Authors: Handing, K.B. / Shabalin, I.G. / Kassaar, O. / Khazaipoul, S. / Blindauer, C.A. / Stewart, A.J. / Chruszcz, M. / Minor, W.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 13, 2017Group: 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 / _citation_author.name
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9303
Polymers65,7681
Non-polymers1612
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.098, 93.098, 141.442
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 / Fragment: residues 25-607 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P35747
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe authors state that in contrast with the previously deposited in PDB structures of Equus ...The authors state that in contrast with the previously deposited in PDB structures of Equus caballus SA (PDB IDs: 3V08, 4J2V, 4OT2, 4F5U, and 4F5T), a single point mutation, R561A, is observed. The long arginine side chain cannot be modeled in this position due to steric clashes with the nearby disulfide bond connecting Cys567 and Cys558 and a symmetry-related copy of the molecule. Moreover, there is no 2mFo-DFc omit map supporting placement of the side chain. Protein was purified from natural source, therefore there may be naturally occurring mutation. According to the NCBI database, this mutation is characteristic for Equus ferus przewalskii, a rare subspecies of wild horse from central Asia (accession code: XP_008524663.1). However it is possible that there is an error in the Equus caballus SA sequence, or the observed mutation naturally occurs in that species.

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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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1 ul of 30 mg/ml protein in 10 mM Tris pH 7.5 and 150 mM NaCl buffer was mixed with 1 ul of the well condition (0.2 M Li2SO4, 0.1 M Tris:HCl pH 7.4, 2.0 M (NH4)2SO4, 5 mM ZnCl2) and ...Details: 1 ul of 30 mg/ml protein in 10 mM Tris pH 7.5 and 150 mM NaCl buffer was mixed with 1 ul of the well condition (0.2 M Li2SO4, 0.1 M Tris:HCl pH 7.4, 2.0 M (NH4)2SO4, 5 mM ZnCl2) and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 26, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50.01 Å / Num. obs: 27051 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/av σ(I): 32.184 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.447.70.965199.3
2.44-2.497.80.799199.5
2.49-2.537.70.704199.5
2.53-2.597.70.585199.5
2.59-2.647.80.494199.5
2.64-2.77.70.456199.6
2.7-2.777.70.372199.5
2.77-2.857.80.323199.6
2.85-2.937.70.26199.7
2.93-3.027.80.186199.5
3.02-3.137.80.151199.9
3.13-3.267.70.115199.7
3.26-3.417.80.089199.7
3.41-3.587.70.071199.7
3.58-3.817.70.062199.8
3.81-4.17.70.052199.7
4.1-4.527.70.046199.8
4.52-5.177.70.042199.7
5.17-6.517.60.042199.9
6.51-507.10.032198.6

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Processing

Software
NameVersionClassification
MD2data collection
SCALEPACKdata scaling
HKL-3000data reduction
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V08

3v08


Resolution: 2.4→50.01 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.937 / SU B: 20.102 / SU ML: 0.218 / SU R Cruickshank DPI: 0.3451 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.345 / ESU R Free: 0.245
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 1348 5 %RANDOM
Rwork0.1748 ---
obs0.1777 25677 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 182.94 Å2 / Biso mean: 72.017 Å2 / Biso min: 36.78 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å21.19 Å20 Å2
2--2.39 Å2-0 Å2
3----7.75 Å2
Refinement stepCycle: final / Resolution: 2.4→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4501 0 6 133 4640
Biso mean--110.06 60.66 -
Num. residues----580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194622
X-RAY DIFFRACTIONr_bond_other_d0.0020.024292
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.9776265
X-RAY DIFFRACTIONr_angle_other_deg0.91839960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1545579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95424.951206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71315795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7321519
X-RAY DIFFRACTIONr_chiral_restr0.0660.2695
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215180
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02973
X-RAY DIFFRACTIONr_mcbond_it7.1134.132319
X-RAY DIFFRACTIONr_mcbond_other7.1134.132318
X-RAY DIFFRACTIONr_mcangle_it8.4636.2072897
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 87 -
Rwork0.293 1913 -
all-2000 -
obs--99.55 %
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)
13.4541-1.7066-0.20937.2978-4.10995.3293-0.05360.28690.10560.22860.1927-0.1041-0.4533-0.1274-0.1390.2170.0957-0.05710.1274-0.02320.2911-46.56138.355-0.681
26.00260.00511.04260.516-1.45494.4105-0.059-0.12660.31130.14470.0204-0.0591-0.4365-0.02890.03860.30270.0888-0.04260.0775-0.0670.3636-40.47345.7390.275
32.95931.3798-4.40916.8645-4.493210.2262-0.12420.0293-0.13520.27590.0813-0.561-0.0414-0.24720.0430.13890.0127-0.15350.2229-0.04840.3217-32.86933.1164.902
45.09150.9005-1.68272.8925-0.80573.5448-0.0536-0.08340.03950.60820.26950.4337-0.2992-0.6777-0.21580.20780.14870.06710.20510.04980.2617-53.2628.0778.663
512.2134-1.0696-6.97371.8230.24627.399-0.119-0.2351-0.62280.55140.02640.30460.0148-0.69280.09270.2560.0170.0450.21810.04750.257-48.19118.6515.914
61.3197-0.2584-0.46471.88090.22281.96120.00570.24170.1489-0.02240.0330.00010.1245-0.2479-0.03860.20480.0167-0.05490.14130.02620.2593-45.04920.579-15.667
73.0173-2.1498-0.65262.46040.40482.9923-0.14030.0406-0.125-0.03210.09010.16160.3191-0.60060.05010.231-0.118-0.08950.14670.00660.2459-49.689.864-17.678
85.8783-0.2779-1.92822.03490.13996.79150.04870.26880.1872-0.2589-0.1436-0.3593-0.20250.44870.09490.3255-0.0360.02540.10370.03950.2788-31.8155.142-21.735
93.1757-0.002-6.54750.09680.402118.7661-0.3519-0.1338-0.355-0.0499-0.1036-0.04970.40850.41370.45550.35880.01660.04980.2080.04750.3041-34.554-4.666-7.861
101.71020.42080.54362.0504-0.12342.68990.09840.13320.01420.057-0.0929-0.21170.24120.1364-0.00540.2050.0132-0.02650.11950.02370.3433-32.0477.1635.999
113.57171.3737-1.0220.67910.50516.50620.614-0.44970.06470.3469-0.1711-0.0640.01760.2792-0.44280.4934-0.1445-0.10580.07820.02370.3849-32.3569.18229.537
124.44530.6889-1.90673.990.84392.95690.272-0.273-0.15240.1419-0.2665-0.10210.19940.1211-0.00560.3386-0.0875-0.08470.08630.04740.239-32.7141.80823.396
134.97890.4829-1.86892.2545-2.97364.79270.2986-0.1669-0.56880.6864-0.5103-0.2023-0.49660.2960.21170.7665-0.4629-0.18670.38280.14310.3351-34.9841.73736.775
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 38
2X-RAY DIFFRACTION2A39 - 89
3X-RAY DIFFRACTION3A90 - 117
4X-RAY DIFFRACTION4A118 - 166
5X-RAY DIFFRACTION5A167 - 206
6X-RAY DIFFRACTION6A207 - 270
7X-RAY DIFFRACTION7A271 - 314
8X-RAY DIFFRACTION8A315 - 364
9X-RAY DIFFRACTION9A365 - 399
10X-RAY DIFFRACTION10A400 - 496
11X-RAY DIFFRACTION11A497 - 517
12X-RAY DIFFRACTION12A518 - 554
13X-RAY DIFFRACTION13A555 - 583

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