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- PDB-5iiu: Crystal structure of Equine Serum Albumin in the presence of 10 m... -

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Basic information

Entry
Database: PDB / ID: 5iiu
TitleCrystal structure of Equine Serum Albumin in the presence of 10 mM zinc at pH 6.9
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 / 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: 2.3 Å
AuthorsHanding, K.B. / Shabalin, I.G. / Cooper, D.R. / Cymborowski, M.T. / 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 23, 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 ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,51812
Polymers65,7681
Non-polymers75011
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.746, 93.746, 141.789
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.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIn contrast with the previously deposited in PDB structures of Equus caballus SA (PDB IDs: 3V08, ...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: 2.73 Å3/Da / Density % sol: 55.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.9
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, 2.0 M (NH4)2SO4, 5 mM ZnCl2, final pH 6.9) 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, 2.0 M (NH4)2SO4, 5 mM ZnCl2, final pH 6.9) and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen). Crystals were soaked with 50 mM ZnCl2 in 100 mM Tris, final pH 6.9, to final concentration of 10 mM

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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: Dec 4, 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: 2.3→80.01 Å / Num. obs: 31099 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 49.5 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/av σ(I): 29.091 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2.3-2.349.4199
2.34-2.389.7199.20.87
2.38-2.439.7199.20.798
2.43-2.489.71990.677
2.48-2.539.71990.576
2.53-2.599.7199.50.497
2.59-2.669.7199.60.407
2.66-2.739.7199.10.355
2.73-2.819.7199.50.303
2.81-2.99.7199.20.258
2.9-39.7199.70.188
3-3.129.7199.50.151
3.12-3.269.7199.50.118
3.26-3.449.8199.50.088
3.44-3.659.7199.40.071
3.65-3.939.7199.70.06
3.93-4.339.7199.50.051
4.33-4.959.7199.40.044
4.95-6.249.6199.40.039
6.24-809.3198.40.028

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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: 5IIH

5iih


Resolution: 2.3→80.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / SU B: 16.572 / SU ML: 0.2 / SU R Cruickshank DPI: 0.2776 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.278 / ESU R Free: 0.224
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 1446 4.7 %RANDOM
Rwork0.1789 ---
obs0.1817 29648 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 153.04 Å2 / Biso mean: 61.773 Å2 / Biso min: 32.33 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20.5 Å20 Å2
2--1.01 Å2-0 Å2
3----3.26 Å2
Refinement stepCycle: final / Resolution: 2.3→80.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 15 193 4722
Biso mean--86.67 55.56 -
Num. residues----581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194667
X-RAY DIFFRACTIONr_bond_other_d0.0080.024324
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.9796301
X-RAY DIFFRACTIONr_angle_other_deg0.91739989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0295580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.13925.024207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02515800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6161518
X-RAY DIFFRACTIONr_chiral_restr0.0680.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215194
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02967
X-RAY DIFFRACTIONr_mcbond_it6.1643.7182323
X-RAY DIFFRACTIONr_mcbond_other6.1653.7172322
X-RAY DIFFRACTIONr_mcangle_it7.6935.5492902
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 101 -
Rwork0.257 2176 -
all-2277 -
obs--98.32 %
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)
16.67091.951.85163.05511.25781.5353-0.2231-0.05650.4786-0.01150.0858-0.0191-0.0878-0.02780.13740.15260.0182-0.03190.22760.03410.167760.091-20.470.879
21.68550.5088-0.16423.45610.9452.0939-0.07710.4533-0.0981-0.19930.2432-0.0060.00070.0871-0.1660.12240.0366-0.00040.32280.00840.086251.19-22.597-7.443
32.0028-0.007-0.18540.6879-0.13011.3048-0.0433-0.0811-0.07170.0394-0.0095-0.12160.29610.20550.05290.17810.003-0.03490.19370.01740.078737.677-31.60412.037
42.6339-1.3444-0.92941.7924-0.0814.43-0.0493-0.25370.23560.1901-0.03350.0714-0.34350.02150.08270.2074-0.0652-0.03970.2013-0.00950.135318.164-26.89520.149
51.19030.38670.35742.04210.26742.4968-0.13010.00470.0732-0.03810.0853-0.02010.0505-0.18290.04480.1706-0.0246-0.01180.2260.00360.090421.289-26.684-6.39
61.4351-0.3373-0.06051.50491.25664.1525-0.21630.27790.0248-0.46430.23340.0159-0.33030.1311-0.01710.238-0.1729-0.00550.209-0.00060.056619.219-27.721-29.584
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 58
2X-RAY DIFFRACTION2A59 - 173
3X-RAY DIFFRACTION3A174 - 320
4X-RAY DIFFRACTION4A321 - 381
5X-RAY DIFFRACTION5A382 - 498
6X-RAY DIFFRACTION6A499 - 583

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