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- PDB-3q8j: Crystal Structure of Asteropsin A from Marine Sponge Asteropus sp. -

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Basic information

Entry
Database: PDB / ID: 3q8j
TitleCrystal Structure of Asteropsin A from Marine Sponge Asteropus sp.
ComponentsAsteropsin A
KeywordsTOXIN / cystine knot / marine sponge / MARINE KNOTTIN
Function / homologyMETHANOL / Asteropsin A
Function and homology information
Biological speciesAsteropus (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 0.87 Å
AuthorsBowling, J.J. / Fronczek, F.R. / Hamann, M.T. / Li, H. / Jung, J.H.
CitationJournal: To be published
Title: An Uncommon Crystal Structure of a Marine Knottin Peptide from Asteropus sp.
Authors: Li, H. / Bowling, J.J. / Fronczek, F.R. / Hong, J. / Hamann, M.T. / Jung, J.H.
History
DepositionJan 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Asteropsin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,25712
Polymers3,9041
Non-polymers35211
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)14.8028, 18.5573, 24.1784
Angle α, β, γ (deg.)83.19, 84.10, 68.04
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide Asteropsin A / ABU8-1


Mass: 3904.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: whole extract / Source: (natural) Asteropus (invertebrata) / References: UniProt: I1SB10
#2: Chemical
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 1.5634 Å3/Da / Density % sol: 21.3237 %
Crystal growTemperature: 295 K / Details: CD3OH-H2O, NMR tube, temperature 295K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.54178 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Nov 5, 2010 / Details: MiraCol capillary optic
RadiationMonochromator: Graphite (002) / Protocol: \f and \w scans / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 0.87→17.15 Å / Num. obs: 27756 / % possible obs: 97.7 % / Redundancy: 2.41 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.68
Reflection shellResolution: 0.87→0.97 Å / Redundancy: 1 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 4.4 / % possible all: 60.5

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
PDB_EXTRACT3.1data extraction
SHELXLrefinement
SHELXL-97refinement
RefinementResolution: 0.87→17.15 Å / Num. parameters: 2725 / Num. restraintsaints: 6 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: 1. Patterson to locate S atoms; 2. The sf file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
all0.0926 27756 --
obs-23213 100 %-
Rfree---RANDOM
Displacement parametersBiso mean: 6.2214 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 238 / Occupancy sum non hydrogen: 302
Refinement stepCycle: LAST / Resolution: 0.87→17.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms270 0 22 10 302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0232
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0
X-RAY DIFFRACTIONs_approx_iso_adps0

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