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- PDB-5ije: Crystal structure of Equine Serum Albumin in the presence of 30 m... -

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Entry
Database: PDB / ID: 5ije
TitleCrystal structure of Equine Serum Albumin in the presence of 30 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 / 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: 2.4 Å
AuthorsHanding, K.B. / Shabalin, I.G. / Cooper, D.R. / Szlachta, K. / 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 1.0Apr 27, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
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)66,71415
Polymers65,7681
Non-polymers94614
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.384, 94.384, 141.905
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.: 13 / 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.: 296 / Source method: isolated from a natural source / Formula: H2O
Compound 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-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: 2.77 Å3/Da / Density % sol: 55.67 %
Description: The author states that two data sets were collected on the same crystal in order to prove the entity and position of metal in the structure. The first data set was collected on the ...Description: The author states that two data sets were collected on the same crystal in order to prove the entity and position of metal in the structure. The first data set was collected on the wavelength above zinc absorption edge and the second below zinc absorption edge.
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, 2.0 M (NH4)2SO4, 5 mM ZnCl2, final pH 7.4) 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 7.4) and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen). Crystals were soaked with 100 mM ZnCl2 in 100 mM Tris, final pH 7.4, to final concentration of 100 mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.282 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 16, 2015 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.4→50.01 Å / Num. obs: 27885 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.042 / Rrim(I) all: 0.09 / Χ2: 1.452 / Net I/av σ(I): 23.03 / Net I/σ(I): 12.4 / Num. measured all: 120428
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.444.10.70713980.7850.3830.8070.77599.9
2.44-2.494.30.6814080.8140.3640.7730.7799.9
2.49-2.534.30.55913780.8780.2980.6350.73999.9
2.53-2.594.30.54513890.8760.2940.6211.074100
2.59-2.644.30.44614020.9120.2390.5080.88299.9
2.64-2.74.30.3714140.9420.1960.420.899.9
2.7-2.774.30.3213890.9440.1690.3630.82499.9
2.77-2.854.40.28413920.9550.1510.3230.89199.9
2.85-2.934.30.21413840.9720.1140.2430.88599.9
2.93-3.024.30.16814070.9830.090.1920.96199.9
3.02-3.134.30.1313840.9880.070.1481.0699.9
3.13-3.264.30.10713960.9910.0570.1221.15199.8
3.26-3.414.40.07814020.9950.0410.0881.22199.7
3.41-3.584.40.06813760.9950.0360.0771.41899.7
3.58-3.814.40.05514030.9970.0290.0631.53299.7
3.81-4.14.40.04914210.9970.0260.0551.75599.6
4.1-4.524.40.04613820.9980.0250.0532.19899.4
4.52-5.174.40.04213890.9980.0230.0482.18399.1
5.17-6.514.40.04813970.9970.0260.0552.74898.7
6.51-504.10.04513740.9970.0250.0525.40994.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SBC-Collectdata collection
HKL-3000data collection
SCALEPACKdata scaling
HKL-3000data reduction
MOLREPphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IIH

5iih


Resolution: 2.4→50.01 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.2426 / WRfactor Rwork: 0.184 / FOM work R set: 0.7597 / SU B: 20.243 / SU ML: 0.244 / SU R Cruickshank DPI: 0.3854 / SU Rfree: 0.2654 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.385 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 1418 5.1 %RANDOM
Rwork0.1954 ---
obs0.1985 26459 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.63 Å2 / Biso mean: 55.396 Å2 / Biso min: 27.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å2-0.55 Å2-0 Å2
2---1.11 Å20 Å2
3---3.6 Å2
Refinement stepCycle: final / Resolution: 2.4→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4463 0 18 296 4777
Biso mean--78.57 50.4 -
Num. residues----581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194624
X-RAY DIFFRACTIONr_bond_other_d0.0020.024282
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.9796235
X-RAY DIFFRACTIONr_angle_other_deg1.30139829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9845580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84824.848198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99815771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5241518
X-RAY DIFFRACTIONr_chiral_restr0.0650.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02964
X-RAY DIFFRACTIONr_mcbond_it2.1231.2252323
X-RAY DIFFRACTIONr_mcbond_other2.1231.2242322
X-RAY DIFFRACTIONr_mcangle_it3.3041.832902
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 79 -
Rwork0.278 1973 -
all-2052 -
obs--99.71 %
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)
111.85892.6452.09864.27220.8562.8079-0.22380.36360.7006-0.0540.13440.0751-0.24520.17440.08950.40850.0380.02990.47470.09760.066660.942-20.36725.129
27.1604-1.73991.55583.3844-1.6284.28440.14760.62150.1249-0.18640.11950.0554-0.243-0.0108-0.26720.4670.0210.11450.48580.06810.080951.453-8.88421.601
35.194-1.0461-0.75072.07540.91621.3994-0.10530.9358-0.3908-0.11580.13430.03690.3070.2034-0.02890.59420.021-0.03340.7904-0.02360.044946.987-32.43616.125
45.113-0.2145-0.46331.0341-0.05321.0748-0.0116-0.35330.06810.2109-0.03070.00710.09750.20170.04230.6102-0.0423-0.03380.61960.08080.016231.198-30.63842.22
51.41770.62571.01542.13011.12183.7498-0.21820.05130.0457-0.1190.13740.0039-0.0088-0.09740.08080.491-0.0586-0.0030.5822-0.01210.002821.253-26.4615.614
61.9267-0.66690.07842.051.52274.8001-0.32910.39550.149-0.48740.37690.0635-0.27020.3177-0.04790.6854-0.2517-0.00590.7236-0.00590.048119.059-29.354-4.872
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 61
2X-RAY DIFFRACTION2A62 - 111
3X-RAY DIFFRACTION3A112 - 209
4X-RAY DIFFRACTION4A210 - 380
5X-RAY DIFFRACTION5A381 - 509
6X-RAY DIFFRACTION6A510 - 583

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