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- PDB-5iix: Crystal structure of Equine Serum Albumin in the presence of 15 m... -

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Basic information

Entry
Database: PDB / ID: 5iix
TitleCrystal structure of Equine Serum Albumin in the presence of 15 mM zinc at pH 6.5
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 / fatty acid binding / cellular response to starvation / pyridoxal phosphate binding / protein-containing complex / extracellular space / DNA binding ...cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / fatty acid binding / cellular response to starvation / pyridoxal phosphate binding / protein-containing complex / extracellular space / 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
Unknown ligand / Albumin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHanding, K.B. / Shabalin, I.G. / Cooper, D.R. / Gasiorowska, O.A. / 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 ...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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_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
Revision 1.6Nov 6, 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

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Assembly

Deposited unit
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,06420
Polymers65,7681
Non-polymers1,29619
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.313, 94.313, 141.485
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.: 11 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
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 6.5) 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 6.5) and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen). Crystals were soaked with 50 mM ZnCl2 in 100 mM Tris, final pH 6.5, to final concentration of 15 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: 2.2→80.01 Å / Num. obs: 36226 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/av σ(I): 31.053 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.247.50.7951100
2.24-2.287.70.7621100
2.28-2.327.70.6161100
2.32-2.377.70.5261100
2.37-2.427.70.4351100
2.42-2.487.70.361100
2.48-2.547.70.3081100
2.54-2.617.70.2661100
2.61-2.697.70.231100
2.69-2.777.70.2021100
2.77-2.877.80.1761100
2.87-2.997.80.137199.9
2.99-3.127.70.115199.9
3.12-3.297.70.0971100
3.29-3.497.70.0781100
3.49-3.767.70.0721100
3.76-4.147.60.0661100
4.14-4.747.50.0621100
4.74-5.977.60.0571100
5.97-807.30.054199.7

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Processing

Software
NameVersionClassification
MD2data collection
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IIH

5iih


Resolution: 2.2→80.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 12.659 / SU ML: 0.167 / SU R Cruickshank DPI: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.192
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 1830 5.1 %RANDOM
Rwork0.1782 ---
obs0.1807 34324 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 151.65 Å2 / Biso mean: 57.969 Å2 / Biso min: 28.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20.48 Å20 Å2
2--0.97 Å2-0 Å2
3----3.13 Å2
Refinement stepCycle: final / Resolution: 2.2→80.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 50 364 4898
Biso mean--76.38 57.3 -
Num. residues----577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194667
X-RAY DIFFRACTIONr_bond_other_d0.0080.024301
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9846291
X-RAY DIFFRACTIONr_angle_other_deg0.92139900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0855575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5624.952208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43115788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4791519
X-RAY DIFFRACTIONr_chiral_restr0.0660.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215164
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02968
X-RAY DIFFRACTIONr_mcbond_it4.6293.382306
X-RAY DIFFRACTIONr_mcbond_other4.6293.3792305
X-RAY DIFFRACTIONr_mcangle_it5.8525.0512879
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 141 -
Rwork0.256 2513 -
all-2654 -
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)
17.40221.18290.86361.42920.50061.1657-0.31490.46850.5181-0.12830.13640.0191-0.16480.16110.17850.1543-0.0322-0.02680.20750.06260.142858.931-20.97123.785
26.4608-6.12783.36485.9193-2.97923.4646-0.4117-0.12910.86690.43770.2074-0.8802-0.41190.13790.20430.1669-0.0177-0.02540.2249-0.04650.194564.853-13.95831.75
35.156-0.6858-1.71574.14732.23572.31520.01020.27030.1793-0.32430.116-0.1024-0.41310.1796-0.12610.22820.0080.07030.15840.04330.099851.963-6.16320.299
46.5247-0.81460.25287.33429.561715.0242-0.21351.04430.2405-0.4251-0.22660.5197-0.5691-0.380.44010.3308-0.0576-0.05730.35160.17930.172741.713-17.93813.232
54.5631-0.5559-4.686610.83722.79366.9835-0.28480.6761-0.1035-0.78990.3201-0.46220.05550.3205-0.03540.0881-0.10540.04390.7886-0.19060.133856.896-34.9038.053
65.2973-0.7157-0.93060.83530.34442.0088-0.2510.657-0.5922-0.05440.11690.08090.26920.25490.13420.1643-0.03620.00440.2576-0.02630.129244.336-31.31318.802
74.80821.15040.36750.91590.35481.1311-0.0793-0.29050.04130.1280.0603-0.06250.09960.05140.0190.14670.0311-0.02830.23150.06760.097441.678-28.95938.735
84.49190.4417-1.93341.7456-0.31534.3298-0.02950.141-0.5125-0.0110.0609-0.27430.4750.1546-0.03150.1770.0431-0.02940.25040.10110.194338.928-41.12238.91
96.89823.97-1.812617.7713.19762.4868-0.0072-1.42250.14530.3164-0.0684-0.0112-0.40610.60450.07560.5408-0.1386-0.22060.5073-0.03940.186219.68-24.23355.31
103.1513-0.4548-1.66971.9407-0.79894.18250.0646-0.27080.21450.3347-0.13130.118-0.4130.17330.06660.2078-0.0636-0.02560.14960.0220.08918.619-27.50344.185
111.15270.04730.28911.11090.37822.1412-0.09840.017-0.08320.12420.0171-0.01180.1296-0.02070.08120.1418-0.06470.01420.1806-0.03110.069720.209-31.28914.389
121.47140.33380.10066.6607-2.02783.5223-0.0627-0.0951-0.02520.0461-0.01030.05750.129-0.11860.07310.1247-0.0021-0.02250.19160.00280.137724.943-24.36622.883
131.54870.01470.25271.38820.55555.1992-0.18110.29880.0297-0.25470.2115-0.0335-0.3798-0.0515-0.03040.1588-0.1678-0.01630.23380.03730.113721.169-23.2693.148
140.97550.16650.87430.74490.23022.3005-0.18680.2908-0.0639-0.28250.25810.0075-0.26550.1876-0.07130.1872-0.16730.00140.2388-0.03160.041216.252-28.255-5.285
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 49
2X-RAY DIFFRACTION2A50 - 71
3X-RAY DIFFRACTION3A72 - 102
4X-RAY DIFFRACTION4A103 - 116
5X-RAY DIFFRACTION5A117 - 136
6X-RAY DIFFRACTION6A137 - 209
7X-RAY DIFFRACTION7A210 - 266
8X-RAY DIFFRACTION8A267 - 306
9X-RAY DIFFRACTION9A307 - 321
10X-RAY DIFFRACTION10A322 - 380
11X-RAY DIFFRACTION11A381 - 437
12X-RAY DIFFRACTION12A438 - 483
13X-RAY DIFFRACTION13A484 - 523
14X-RAY DIFFRACTION14A524 - 583

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