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- PDB-5xn9: Crystal structure of a secretary abundant heat soluble (SAHS) pro... -

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Basic information

Entry
Database: PDB / ID: 5xn9
TitleCrystal structure of a secretary abundant heat soluble (SAHS) protein from Ramazzottius varieornatus (from monomer 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 / Secretory-abundant heat soluble protein 1
Function and homology information
Biological speciesRamazzottius varieornatus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.449 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.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.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.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)33,75026
Polymers32,3822
Non-polymers1,36824
Water3,837213
1
A: SAHS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,74811
Polymers16,1911
Non-polymers55810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAHS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,00115
Polymers16,1911
Non-polymers81114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.866, 57.505, 111.723
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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: J7MFT5

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Non-polymers , 6 types, 237 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 12 mg/mL protein, 100 mM HEPES pH 7.8, 150 mM MgCl2, 1 mM ZnSO4, 3.0% v/v 2-propanol, 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: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.449→50 Å / Num. obs: 62308 / % possible obs: 99.9 % / Redundancy: 11.8 % / Rrim(I) all: 0.077 / Net I/σ(I): 42.3
Reflection shellResolution: 1.449→1.48 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3067 / CC1/2: 0.786 / Rrim(I) all: 0.933 / % possible all: 100

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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: 1.449→31.259 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.78
RfactorNum. reflection% reflection
Rfree0.1719 2003 3.22 %
Rwork0.1448 --
obs0.1457 62235 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.449→31.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 72 213 2570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052656
X-RAY DIFFRACTIONf_angle_d0.7633578
X-RAY DIFFRACTIONf_dihedral_angle_d23.329988
X-RAY DIFFRACTIONf_chiral_restr0.09341
X-RAY DIFFRACTIONf_plane_restr0.005476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4494-1.48570.2161500.18874181X-RAY DIFFRACTION98
1.4857-1.52580.20251270.17554230X-RAY DIFFRACTION100
1.5258-1.57070.21961500.15334278X-RAY DIFFRACTION100
1.5707-1.62140.16551420.13294234X-RAY DIFFRACTION100
1.6214-1.67940.17431330.13064298X-RAY DIFFRACTION100
1.6794-1.74660.16221410.11894279X-RAY DIFFRACTION100
1.7466-1.82610.15861480.12284260X-RAY DIFFRACTION100
1.8261-1.92240.17771360.12564307X-RAY DIFFRACTION100
1.9224-2.04280.14561530.12464262X-RAY DIFFRACTION100
2.0428-2.20050.15431370.13844313X-RAY DIFFRACTION100
2.2005-2.42180.1631430.14454324X-RAY DIFFRACTION100
2.4218-2.77210.19861460.16114339X-RAY DIFFRACTION100
2.7721-3.49180.19851450.15644396X-RAY DIFFRACTION100
3.4918-31.26580.15381520.14344531X-RAY DIFFRACTION99

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