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- PDB-1j6z: UNCOMPLEXED ACTIN -

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Basic information

Entry
Database: PDB / ID: 1j6z
TitleUNCOMPLEXED ACTIN
ComponentsACTIN ALPHA 1
KeywordsCONTRACTILE PROTEIN / ACTIN / TETRAMETHYLRHODAMINE-5-MALEIMIDE / ADP-STATE
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'-DIPHOSPHATE / TETRAMETHYLRHODAMINE-5-MALEIMIDE / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsOtterbein, L.R. / Graceffa, P. / Dominguez, R.
CitationJournal: Science / Year: 2001
Title: The crystal structure of uncomplexed actin in the ADP state.
Authors: Otterbein, L.R. / Graceffa, P. / Dominguez, R.
History
DepositionMay 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 16, 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.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 THE LIGAND RHO IS MISSING SOME ATOMS DUE TO LACK OF ELECTRON DENSITY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACTIN ALPHA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0279
Polymers41,8761
Non-polymers1,1518
Water7,278404
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.808, 37.498, 85.261
Angle α, β, γ (deg.)90.00, 108.26, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUE HIS A 73 IS A METHYLATED HISTIDINE.

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Components

#1: Protein ACTIN ALPHA 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.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-RHO / TETRAMETHYLRHODAMINE-5-MALEIMIDE / TMR


Mass: 483.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H25N3O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 2000 MONOMETHYLETHER 22%, CALCIUM ACETATE 200mM, TRIS 10mM (pH 7), pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
222 %PEG2000 MME1reservoir
310 mMTris1reservoirpH7.0
4200 mMcalcium acetate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONAPS 14-BM-C111
SYNCHROTRONAPS 17-ID21
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDDec 7, 2000BENT CONICAL SI-MIRROR
MARRESEARCH2CCDSep 2, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1BEND CYLINDRICAL GE(III)SINGLE WAVELENGTHMx-ray1
2CRYOGENICALLY COOLED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.54→82 Å / Num. all: 48139 / Num. obs: 48139 / % possible obs: 96.6 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.3
Reflection shellResolution: 1.54→1.61 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.308 / Num. unique all: 4665 / % possible all: 94.2
Reflection
*PLUS
% possible obs: 97 %

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
WARPmodel building
REFMACrefinement
HKL-2000data scaling
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ATN.PDB

1atn


Resolution: 1.54→82 Å / Data cutoff low absF: 20 / Cross valid method: FREE R-FACTOR / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2435 5 %reflections randomly selected
Rwork0.179 ---
all0.179 48118 --
obs0.179 48118 97 %-
Displacement parametersBiso mean: 18.27 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.54→82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2884 0 63 404 3351
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_improper_angle_d2.08
LS refinement shellResolution: 1.543→1.618 Å
RfactorNum. reflection% reflection
Rfree0.242 297 5 %
Rwork0.201 5950 -
obs-5479 84.6 %
Software
*PLUS
Name: WARP-REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg25
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg2.08

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