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- PDB-1s22: Absolute Stereochemistry of Ulapualide A -

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Basic information

Entry
Database: PDB / ID: 1s22
TitleAbsolute Stereochemistry of Ulapualide A
ComponentsActin
KeywordsSTRUCTURAL PROTEIN / actin / trisoxazole / macrolide / toxin / ulapualide / stereochemistry
Function / homology
Function and homology information


cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. ...Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ULAPUALIDE A / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAllingham, J.S. / Tanaka, J. / Marriott, G. / Rayment, I.
CitationJournal: Org.Lett. / Year: 2004
Title: Absolute stereochemistry of ulapualide A
Authors: Allingham, J.S. / Tanaka, J. / Marriott, G. / Rayment, I.
History
DepositionJan 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4306
Polymers41,8761
Non-polymers1,5545
Water6,882382
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.8, 75.2, 67.5
Angle α, β, γ (deg.)90.00, 100.2, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Actin / / Actin / alpha skeletal muscle / Alpha-actin 1


Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: complexed with Ulapualide A, residue ULA / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135

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Non-polymers , 5 types, 387 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-ULA / ULAPUALIDE A


Mass: 883.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H66N4O13
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.23 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293 K / Method: batch / pH: 6
Details: 100 mM MES, 15% methyl ether poly(ethylene glycol) 5000, 75 mM CaCl2, 1 mM sodium azide, 1 mM TCEP, pH 6.0, Batch, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMMES11pH6.0
215 %MPEG500011
375 mM11CaCl2
41 mMsodium azide11
51 mMTCEP11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.964 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 4, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 1.6→65.94 Å / Num. all: 52947 / Num. obs: 52947 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 36.5
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 5.2 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å / Num. measured all: 216388
Reflection shell
*PLUS
Highest resolution: 1.6 Å / % possible obs: 99.9 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
REFMAC5refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QZ6

1qz6


Resolution: 1.6→65.94 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.272 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.074 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17903 2690 5.1 %RANDOM
Rwork0.152 ---
all0.15338 52947 --
obs0.15338 50233 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.19 Å2
2--0.2 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.6→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 90 387 3260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212936
X-RAY DIFFRACTIONr_bond_other_d0.0020.022642
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9923985
X-RAY DIFFRACTIONr_angle_other_deg1.73236160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5475355
X-RAY DIFFRACTIONr_chiral_restr0.1010.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023187
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02560
X-RAY DIFFRACTIONr_nbd_refined0.2090.2935
X-RAY DIFFRACTIONr_nbd_other0.2490.23337
X-RAY DIFFRACTIONr_nbtor_other0.1620.22482
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2259
X-RAY DIFFRACTIONr_metal_ion_refined0.0830.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3710.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.222
X-RAY DIFFRACTIONr_mcbond_it0.831.51782
X-RAY DIFFRACTIONr_mcangle_it1.48422891
X-RAY DIFFRACTIONr_scbond_it2.48631154
X-RAY DIFFRACTIONr_scangle_it4.0924.51094
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.238 203
Rwork0.191 3693
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.67
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.66 Å

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