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- PDB-1pne: CRYSTALLIZATION AND STRUCTURE DETERMINATION OF BOVINE PROFILIN AT... -

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Basic information

Entry
Database: PDB / ID: 1pne
TitleCRYSTALLIZATION AND STRUCTURE DETERMINATION OF BOVINE PROFILIN AT 2.0 ANGSTROMS RESOLUTION
ComponentsPROFILIN
KeywordsACTIN BINDING PROTEIN
Function / homology
Function and homology information


PCP/CE pathway / RHO GTPases Activate Formins / positive regulation of actin filament bundle assembly / regulation of actin filament polymerization / actin binding / actin cytoskeleton organization / cytoskeleton / cytoplasm
Similarity search - Function
Profilin1/2/3, vertebrate / Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase ...Profilin1/2/3, vertebrate / Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsCedergren-Zeppezauer, E.S. / Goonesekere, N.C.W. / Rozycki, M.D. / Myslik, J.C. / Dauter, Z. / Lindberg, U. / Schutt, C.E.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and structure determination of bovine profilin at 2.0 A resolution.
Authors: Cedergren-Zeppezauer, E.S. / Goonesekere, N.C. / Rozycki, M.D. / Myslik, J.C. / Dauter, Z. / Lindberg, U. / Schutt, C.E.
#1: Journal: Curr.Opin.Struct.Biol. / Year: 1994
Title: Structural Aspects of Actin-Binding Proteins
Authors: Rozycki, M.D. / Myslik, J.C. / Schutt, C.E. / Lindberg, U.
#2: Journal: Nature / Year: 1993
Title: The Structure of Crystalline Profilin-Beta-Actin
Authors: Schutt, C.E. / Myslik, J.C. / Rozycki, M.D. / Goonesekere, N.C.W. / Lindberg, U.
#3: Journal: FEBS Lett. / Year: 1993
Title: Mutagenesis of Human Profilin Locates its Poly(L-Proline)-Binding Site to a Hydrophobic Patch of Aromatic Amino Acids
Authors: Bjorkegren, C. / Rozycki, M. / Schutt, C.E. / Lindberg, U. / Karlsson, R.
History
DepositionMay 5, 1995Processing site: BNL
Revision 1.0Jul 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag
Remark 700SHEET PROFILIN IS DESCRIBED IN JRNL REFERENCE AS HAVING A 6-MEMBERED BETA-SHEET WHICH SHARES A ...SHEET PROFILIN IS DESCRIBED IN JRNL REFERENCE AS HAVING A 6-MEMBERED BETA-SHEET WHICH SHARES A STRAND WITH A SECOND 2-MEMBERED SHEET. TO CONFORM WITH PDB GUIDELINES, THESE SHEETS ARE COMBINED INTO A SINGLE 7-MEMBERED SHEET (SP1) IN THIS FILE. STRAND NUMBERING ALSO DIFFERS FROM THE JRNL REFERENCE. RESIDUES TRP 31 AND ILE 73 ADOPT BETA-BULGE CONFORMATIONS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROFILIN


Theoretical massNumber of molelcules
Total (without water)14,9681
Polymers14,9681
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.150, 34.590, 52.490
Angle α, β, γ (deg.)90.00, 92.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROFILIN


Mass: 14968.185 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P02584
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGAMMA-TURN AT RESIDUES 25 - 27 DOES NOT HAVE THE CANONICAL I TO I+2 HYDROGEN BOND, SINCE CARBONYL O ...GAMMA-TURN AT RESIDUES 25 - 27 DOES NOT HAVE THE CANONICAL I TO I+2 HYDROGEN BOND, SINCE CARBONYL O OF LYS 25 IS HYDROGEN BONDED TO WATER MOLECULE 27. WATER MOLECULE 27 IS BONDED TO WATER MOLECULE 28, WHICH IN TURN IS BOUND TO THE CARBONYL O OF SER 27. THE INVOLVEMENT OF WATER 28 WAS NOT DISCUSSED IN THE TEXT OR IN FIGURE 9 OF THE JRNL REFERENCE. TURN T8 IS A TYPE I TURN AS JUDGED BY PHI-PSI ANGLES FOR RESIDUES ALA 96 AND LYS 97. HOWEVER, THE NORMAL I TO I+3 HYDROGEN BOND IS NOT MADE. INSTEAD, THE CARBONYL OXYGEN OF THR 95 IS HYDROGEN BONDED TO THE PHENOLIC HYDROXYL OF TYR 24.
Has protein modificationY
Sequence detailsSEQUENCE IDENTIFIERS ARE NUMBERED 1 THROUGH 139 FOR STANDARD AMINO ACID RESIDUES. THE N-TERMINAL ...SEQUENCE IDENTIFIERS ARE NUMBERED 1 THROUGH 139 FOR STANDARD AMINO ACID RESIDUES. THE N-TERMINAL ACETYL GROUP IS PLACED AT THE BEGINNING OF THE SEQUENCE AS A SEPARATE RESIDUE (ACE) AND IS NUMBERED "0".

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 %PEG4001reservoir
22.0 Mammonium sulfate1reservoir
310 mMbeta-mercaptoethanol1reservoir
40.1 MHEPES1drop
514 mg/mlprofilin1drop

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Data collection

DetectorDate: 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 8239 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 3.56 % / Rmerge(I) obs: 0.066
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 29297 / Rmerge(I) obs: 0.066

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data reduction
X-PLORphasing
RefinementResolution: 2→6 Å / σ(F): 3
Details: RESIDUES ARE INCLUDED AT THE BEGINNING OF HELICES IF THEY PARTICIPATE IN HYDROGEN BONDING AND ARE "PARTIALLY" HELICAL, EVEN IF THE ENTIRE RESIDUE DOES NOT FIT HELICAL CRITERIA.
RfactorNum. reflection
Rwork0.165 -
obs0.165 7898
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 0 127 1174
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.54
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.99
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.99

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