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- PDB-2fxu: X-ray Structure of Bistramide A- Actin Complex at 1.35 A resolution. -

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Basic information

Entry
Database: PDB / ID: 2fxu
TitleX-ray Structure of Bistramide A- Actin Complex at 1.35 A resolution.
ComponentsActin, alpha skeletal muscle
KeywordsSTRUCTURAL PROTEIN / Actin complexed to Bistramide A
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
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 ...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 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / BISTRAMIDE A / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsRizvi, S.A. / Tereshko, V. / Kossiakoff, A.A. / Kozmin, S.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Structure of bistramide a-actin complex at a 1.35 A resolution
Authors: Rizvi, S.A. / Tereshko, V. / Kossiakoff, A.A. / Kozmin, S.A.
History
DepositionFeb 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN WHILE THE C(19)-C(40) SPIROKETAL AND THE C(14)-C(18) AMINO ACID SUBUNITS OF BISTRAMIDE A ...HETEROGEN WHILE THE C(19)-C(40) SPIROKETAL AND THE C(14)-C(18) AMINO ACID SUBUNITS OF BISTRAMIDE A ARE HIGHLY ORDERED, THE C(1)-C(4) ENONE SIDE CHAIN ATTACHED TO THE PYRAN FRAGMENT IS DISORDERED. THE C(5), C(4) AND O(1) ATOMS ARE PLACED BASED ON THE DIFFERENCE ELECTRON DENSITY MAP F(OBS)-F(CALC) AND HAVE OCCUPANCY 0.5. THE C(1)-C(3) ATOMS ARE INCLUDED IN THE PDB ENTRY IN THE CALCULATED POSITIONS WITH THE OCCUPANCY EQUAL TO 0.0

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2487
Polymers41,8761
Non-polymers1,3726
Water7,602422
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.125, 56.513, 101.652
Angle α, β, γ (deg.)90.00, 94.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-377-

CA

21A-420-

HOH

31A-422-

HOH

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Components

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


Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MUSCLE / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / 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-BID / BISTRAMIDE A / (2S,3R)-3-HYDROXY-N-(3-{(2R,3S,6S,8S)-8-[(3S,4E,6S)-6-HYDROXY-3,5-DIMETHYLHEPT-4-EN-1-YL]-3-METHYL-1,7-DIOXASPIRO[5.5]U NDEC-2-YL}PROPYL)-2-METHYL-4-[({(2S,3S,6R)-3-METHYL-6-[(3E)-2-OXOPENT-3-EN-1-YL]TETRAHYDRO-2H-PYRAN-2-YL}ACETYL)AMINO]BU TANAMIDE / Bistramide A


Mass: 704.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H68N2O8 / Comment: toxin*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.06 Å3/Da / Density % sol: 40.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: The bistramide A- actin complex was mixed with the crystallization buffer in 1:1 ratio. The crystallization buffer is 100 mM MES (ph 6.0), 24% (w/v) PEG1500, 70 mM CaCl2, 1mM NaN3, 1mM TCEP. ...Details: The bistramide A- actin complex was mixed with the crystallization buffer in 1:1 ratio. The crystallization buffer is 100 mM MES (ph 6.0), 24% (w/v) PEG1500, 70 mM CaCl2, 1mM NaN3, 1mM TCEP., VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 27, 2005 / Details: mirrors
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 72741 / Num. obs: 72741 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 27.6
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.6 / Num. unique all: 6029 / % possible all: 81.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code: 1J6Z
Resolution: 1.35→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.008 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.059 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20148 3681 5.1 %RANDOM
Rwork0.17431 ---
all0.17571 72716 --
obs0.17571 72716 97.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.839 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å21.08 Å2
2--0.12 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 85 422 3329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222984
X-RAY DIFFRACTIONr_bond_other_d0.0010.022704
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9984054
X-RAY DIFFRACTIONr_angle_other_deg1.15936312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8295359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96224.252127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1615502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1551517
X-RAY DIFFRACTIONr_chiral_restr0.0950.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023241
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02575
X-RAY DIFFRACTIONr_nbd_refined0.2170.2641
X-RAY DIFFRACTIONr_nbd_other0.1830.22910
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21488
X-RAY DIFFRACTIONr_nbtor_other0.0850.21678
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0980.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0760.23
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0581.51851
X-RAY DIFFRACTIONr_mcbond_other0.2691.5731
X-RAY DIFFRACTIONr_mcangle_it1.47622918
X-RAY DIFFRACTIONr_scbond_it2.35131298
X-RAY DIFFRACTIONr_scangle_it3.2954.51136
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.401 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.281 325 -
Rwork0.258 6061 -
obs--81.77 %
Refinement TLS params.Method: refined / Origin x: 18.1975 Å / Origin y: -0.7607 Å / Origin z: 25.1161 Å
111213212223313233
T-0.0147 Å2-0.0194 Å20.0026 Å2--0.0032 Å2-0.0128 Å2---0.0167 Å2
L0.5747 °20.0635 °2-0.1158 °2-0.5979 °2-0.1036 °2--0.7877 °2
S0.0517 Å °-0.1191 Å °0.0137 Å °0.1568 Å °-0.0402 Å °0.0521 Å °-0.0326 Å °-0.1031 Å °-0.0115 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 371
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION1A423 - 824

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