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Basic information

Entry
Database: PDB / ID: 5z4g
TitleCrystal structure of secretory abundant heat soluble protein 4 from Ramazzottius varieornatus
ComponentsSAHS4
KeywordsUNKNOWN FUNCTION / tardigrade
Function / homologyCalycin / TRIETHYLENE GLYCOL / SAHS4
Function and homology information
Biological speciesRamazzottius varieornatus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFukuda, Y. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS Japan
CitationJournal: Protein Sci. / Year: 2018
Title: Crystal structure of secretory abundant heat soluble protein 4 from one of the toughest "water bears" micro-animals Ramazzottius Varieornatus
Authors: Fukuda, Y. / Inoue, T.
History
DepositionJan 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: SAHS4
B: SAHS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5878
Polymers36,9812
Non-polymers6066
Water5,531307
1
A: SAHS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8164
Polymers18,4901
Non-polymers3253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-36 kcal/mol
Surface area8750 Å2
MethodPISA
2
B: SAHS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7714
Polymers18,4901
Non-polymers2813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-35 kcal/mol
Surface area8520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.802, 41.926, 53.483
Angle α, β, γ (deg.)89.97, 80.75, 78.76
Int Tables number1
Space group name H-MP1

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Components

#1: Protein SAHS4


Mass: 18490.477 Da / Num. of mol.: 2 / Fragment: UNP residues 28-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ramazzottius varieornatus (invertebrata)
Gene: RvY_02365-1, RvY_02365.1, RvY_02365 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1D1UN89
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 1.92 Å3/Da / Density % sol: 36.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 50mM HEPES pH 7.8, 1mM ZnSO4, 24%(v/v) PEG600

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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: Oct 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→50.01 Å / Num. obs: 42396 / % possible obs: 95.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.036 / Rrim(I) all: 0.051 / Net I/σ(I): 23.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2099 / CC1/2: 0.818 / Rpim(I) all: 0.26 / Rrim(I) all: 0.368 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XNA

5xna


Resolution: 1.5→50.01 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.084 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20308 2077 4.9 %RANDOM
Rwork0.15945 ---
obs0.16161 40319 95.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.76 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.5→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 27 307 2658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192657
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9263627
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6345335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34425.868121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38815468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.478152
X-RAY DIFFRACTIONr_chiral_restr0.0750.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212058
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.492.0041277
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.252.9971633
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6922.3431380
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.20318.6434196
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.9132657
X-RAY DIFFRACTIONr_sphericity_free28.975597
X-RAY DIFFRACTIONr_sphericity_bonded17.68652783
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 147 -
Rwork0.203 2913 -
obs--93.81 %

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