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- PDB-5xna: Crystal structure of a secretary abundant heat soluble (SAHS) pro... -

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Basic information

Entry
Database: PDB / ID: 5xna
TitleCrystal structure of a secretary abundant heat soluble (SAHS) protein from Ramazzottius varieornatus (from dimer sample)
ComponentsSAHS1
KeywordsLIPID TRANSPORT / secretary abundant heat soluble protein / Ramazzottius varieornatus / fatty acid binding protein
Function / homologyCytosolic fatty-acid binding / Calycin / lipid binding / extracellular region / ACETIC ACID / HEPTANOIC ACID / Secretory-abundant heat soluble protein 1
Function and homology information
Biological speciesRamazzottius varieornatus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsFukuda, Y. / Miura, Y. / Mizohata, E. / Inoue, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS16H06940 Japan
JSPS17K17862 Japan
CitationJournal: FEBS Lett. / Year: 2017
Title: Structural insights into a secretory abundant heat-soluble protein from an anhydrobiotic tardigrade, Ramazzottius varieornatus
Authors: Fukuda, Y. / Miura, Y. / Mizohata, E. / Inoue, T.
History
DepositionMay 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Aug 28, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAHS1
B: SAHS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,95328
Polymers32,3822
Non-polymers1,57126
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-165 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.672, 57.799, 110.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SAHS1 / Secretary abundant heat soluble protein 1


Mass: 16190.857 Da / Num. of mol.: 2 / Fragment: UNP residues 31-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ramazzottius varieornatus (invertebrata)
Gene: SAHS1, RvY_02423-1, RvY_02423.1, RvY_02423 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: J7MFT5

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Non-polymers , 7 types, 221 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SHV / HEPTANOIC ACID


Mass: 130.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O2
#7: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 11 mg/mL protein, 100 mM HEPES pH 7.8, 150 mM MgCl2, 1 mM ZnSO4, 5.0% v/v 1-butanol, and 21% v/v PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 32203 / % possible obs: 98.5 % / Redundancy: 7.3 % / Rrim(I) all: 0.059 / Net I/σ(I): 37.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 6 / Num. unique obs: 1580 / CC1/2: 0.974 / Rrim(I) all: 0.267 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.802→31.143 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.53
RfactorNum. reflection% reflection
Rfree0.2387 1630 5.07 %
Rwork0.1857 --
obs0.1884 32147 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.802→31.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2278 0 79 195 2552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062597
X-RAY DIFFRACTIONf_angle_d0.8363493
X-RAY DIFFRACTIONf_dihedral_angle_d18.111510
X-RAY DIFFRACTIONf_chiral_restr0.062331
X-RAY DIFFRACTIONf_plane_restr0.005462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8015-1.85460.26351410.20372461X-RAY DIFFRACTION97
1.8546-1.91440.27421490.20512474X-RAY DIFFRACTION98
1.9144-1.98280.28131450.19632491X-RAY DIFFRACTION98
1.9828-2.06220.21931330.19092518X-RAY DIFFRACTION98
2.0622-2.1560.23111190.19632511X-RAY DIFFRACTION99
2.156-2.26970.23691330.19162536X-RAY DIFFRACTION99
2.2697-2.41180.2651250.20242546X-RAY DIFFRACTION99
2.4118-2.59790.25921260.20712554X-RAY DIFFRACTION100
2.5979-2.85920.25831480.20122562X-RAY DIFFRACTION99
2.8592-3.27260.25551130.20042609X-RAY DIFFRACTION99
3.2726-4.12160.2231470.16882623X-RAY DIFFRACTION99
4.1216-31.14720.21521510.16342632X-RAY DIFFRACTION96

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