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- PDB-5hoz: Crystal structure of Equine Serum Albumin (ESA) at pH 9.0 -

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Basic information

Entry
Database: PDB / ID: 5hoz
TitleCrystal structure of Equine Serum Albumin (ESA) at pH 9.0
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / albumin / ESA / pH / 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: 2.15 Å
AuthorsHanding, K.B. / Shabalin, I.G. / Minor, W. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal structure of Equine Serum Albumin (ESA) at pH 9.0
Authors: Handing, K.B. / Shabalin, I.G. / Minor, W. / Almo, S.C.
History
DepositionJan 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Data collection
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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


Theoretical massNumber of molelcules
Total (without water)65,7681
Polymers65,7681
Non-polymers00
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.825, 93.825, 141.348
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 / Mutation: R561A / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P35747
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 54.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 1 ul of 32 mg/ml protein in 10 mM Tris pH 7.5, 150 mM NaCl was mixed with 1 ul of the well condition (100 mM Tris, 2.4 M Ammonium phosphate, final pH 9.0) and equilibrated against well ...Details: 1 ul of 32 mg/ml protein in 10 mM Tris pH 7.5, 150 mM NaCl was mixed with 1 ul of the well condition (100 mM Tris, 2.4 M Ammonium phosphate, final pH 9.0) and equilibrated against well solution on 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: Apr 16, 2015 / 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: 2.15→80.01 Å / Num. obs: 37617 / % possible obs: 98.1 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/av σ(I): 23.864 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.15-2.194.70.7371.8194.3
2.19-2.2350.616197.1
2.23-2.275.20.525197.6
2.27-2.325.20.488197.5
2.32-2.375.20.382197.9
2.37-2.425.20.331198.1
2.42-2.485.20.275197.8
2.48-2.555.20.225198.2
2.55-2.625.20.182198.2
2.62-2.715.20.156198.2
2.71-2.815.20.133198.5
2.81-2.925.20.106198.6
2.92-3.055.20.075198.6
3.05-3.215.20.059198.6
3.21-3.415.20.045199
3.41-3.685.20.039199
3.68-4.055.10.036199
4.05-4.635.10.03199.3
4.63-5.845.10.028199.3
5.84-804.90.025196.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.15data extraction
HKL-3000phasing
Cootmodel building
MOLREPphasing
HKL-3000data reduction
MD2data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DQF

5dqf


Resolution: 2.15→80.01 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 13.678 / SU ML: 0.174 / SU R Cruickshank DPI: 0.2259 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.19
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. There are four disordered loops in the structure: 54-66, 105-122, 166-176, 360-365 that contribute to higher than average RSRZ value.
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 1761 4.7 %RANDOM
Rwork0.1955 ---
obs0.1975 35855 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 158.48 Å2 / Biso mean: 66.867 Å2 / Biso min: 33.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20.85 Å20 Å2
2--1.69 Å2-0 Å2
3----5.49 Å2
Refinement stepCycle: final / Resolution: 2.15→80.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4407 0 0 299 4706
Biso mean---62.62 -
Num. residues----572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194517
X-RAY DIFFRACTIONr_bond_other_d0.0030.024195
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9756129
X-RAY DIFFRACTIONr_angle_other_deg0.96939715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0455569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77624.772197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55715761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0211519
X-RAY DIFFRACTIONr_chiral_restr0.0750.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215073
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02962
X-RAY DIFFRACTIONr_mcbond_it5.8143.2932285
X-RAY DIFFRACTIONr_mcbond_other5.8163.2942284
X-RAY DIFFRACTIONr_mcangle_it7.1184.9222851
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 116 -
Rwork0.306 2575 -
all-2691 -
obs--95.09 %
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)
11.6485-2.8258-0.97978.4392-0.18952.2024-0.02860.08120.24840.41790.22130.106-0.7578-0.5839-0.19270.56750.3162-0.18670.3341-0.01990.5026-47.74838.41-27.994
27.8255-0.89891.32775.2859-5.71686.74860.21660.15711.0116-0.14990.1090.11060.36330.032-0.32570.37270.1864-0.15360.1258-0.13970.4562-45.71846.043-25.149
30.20020.1089-0.96253.6011-1.37737.11650.1238-0.0790.03590.11380.0630.1507-0.26740.1826-0.18680.28040.0994-0.1330.2529-0.13620.4026-33.59237.2-18.337
45.5311-0.9721-2.80542.87840.46482.8725-0.1651-0.3892-0.00040.66520.21460.435-0.1246-0.6597-0.04940.27270.21340.03990.5676-0.00350.3373-52.69724.475-16.113
51.789-1.45010.59772.0204-1.21732.3721-0.080.05460.0679-0.11040.13720.05750.2386-0.4497-0.05710.1226-0.0174-0.0650.1352-0.02510.2545-46.81117.142-39.693
62.4884-0.49830.34411.2794-0.88847.77180.15070.44840.0072-0.3095-0.3577-0.20471.08440.63640.20690.38770.162-0.01370.17170.00880.2468-31.7242.201-44.989
71.4838-0.33470.33051.6617-1.34542.5897-0.04660.0416-0.1865-0.10140.0344-0.04740.328-0.14120.01210.16530.0151-0.02940.0817-0.01710.3164-33.2585.706-17.727
82.75770.3534-1.67142.79562.01863.72470.2788-0.1584-0.11450.4315-0.0987-0.23620.18340.0513-0.180.2245-0.0107-0.08040.07990.05830.3062-32.5414.9340.761
93.6897-0.4883-3.03147.56361.36739.81850.7323-0.3195-0.4771.4532-0.9922-0.54060.0789-0.11040.261.5392-0.6599-0.47650.31680.26960.4831-36.161.18811.506
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 32
2X-RAY DIFFRACTION2A33 - 68
3X-RAY DIFFRACTION3A69 - 117
4X-RAY DIFFRACTION4A118 - 202
5X-RAY DIFFRACTION5A203 - 310
6X-RAY DIFFRACTION6A311 - 387
7X-RAY DIFFRACTION7A388 - 497
8X-RAY DIFFRACTION8A498 - 547
9X-RAY DIFFRACTION9A548 - 583

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