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- PDB-3d9y: Crystal Structure of Profilin from Schizosaccharomyces pombe -

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Basic information

Entry
Database: PDB / ID: 3d9y
TitleCrystal Structure of Profilin from Schizosaccharomyces pombe
ComponentsProfilin
KeywordsPROTEIN BINDING / profilin / pombe / Yeast / Actin-binding / Cytoskeleton
Function / homology
Function and homology information


cytogamy / actin cortical patch organization / medial cortex / mitotic actomyosin contractile ring assembly / cell cortex of cell tip / sequestering of actin monomers / actin cortical patch / mating projection tip / actin monomer binding / actin filament polymerization ...cytogamy / actin cortical patch organization / medial cortex / mitotic actomyosin contractile ring assembly / cell cortex of cell tip / sequestering of actin monomers / actin cortical patch / mating projection tip / actin monomer binding / actin filament polymerization / guanyl-nucleotide exchange factor activity / cell cortex
Similarity search - Function
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 speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsEzezika, O.C. / Nolen, B.J. / Pollard, T.D.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Incompatibility with Formin Cdc12p Prevents Human Profilin from Substituting for Fission Yeast Profilin: INSIGHTS FROM CRYSTAL STRUCTURES OF FISSION YEAST PROFILIN.
Authors: Ezezika, O.C. / Younger, N.S. / Lu, J. / Kaiser, D.A. / Corbin, Z.A. / Nolen, B.J. / Kovar, D.R. / Pollard, T.D.
History
DepositionMay 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Profilin
B: Profilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0294
Polymers26,8452
Non-polymers1842
Water4,774265
1
A: Profilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5142
Polymers13,4221
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Profilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5142
Polymers13,4221
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.533, 84.021, 40.420
Angle α, β, γ (deg.)90.000, 93.730, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: 1 / Auth seq-ID: 24 - 30 / Label seq-ID: 25 - 31

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsTwo biological units in the assymetric unit

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Components

#1: Protein Profilin


Mass: 13422.347 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: cdc3, SPAC4A8.15c / Plasmid: pMW-SpPRF / Production host: Escherichia coli (E. coli) / Strain (production host): B21 (DE3) / References: UniProt: P39825
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.3 M Na Malonate; 0.2 M Hepes pH 7.0; 0.5% JeffamineED2001 [O O'-BIS (2-aminopropyl) polyethylene glycol 1900] from Hampton Research], VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12731
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU 20011.54178
SYNCHROTRONNSLS X29A21.0809
Detector
TypeIDDetectorDate
MAR scanner 345 mm plate1IMAGE PLATEOct 2, 2006
MARRESEARCH2CCDJul 24, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror.
Radiation wavelength
IDWavelength (Å)Relative weight
11.541781
21.08091
ReflectionResolution: 1.65→50 Å / Num. all: 59358 / Num. obs: 24741 / % possible obs: 92 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.039 / Rsym value: 0.048 / Net I/σ(I): 19.3
Reflection shellResolution: 1.65→1.81 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.23 / Num. unique all: 1783 / Rsym value: 0.17 / % possible all: 73.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.464 / Cor.coef. Fo:Fc: 0.492
Highest resolutionLowest resolution
Rotation3 Å29.09 Å
Translation3 Å29.09 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ACG

2acg


Resolution: 1.65→42 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.275 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1262 5.1 %RANDOM
Rwork0.175 ---
all0.177 ---
obs0.177 24740 84.86 %-
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: 15.225 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å2-0.85 Å2
2---1.37 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.65→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 12 265 2143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221924
X-RAY DIFFRACTIONr_bond_other_d0.0010.021796
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9712610
X-RAY DIFFRACTIONr_angle_other_deg0.81634166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0455252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25723.91369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02615306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.438159
X-RAY DIFFRACTIONr_chiral_restr0.2520.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022153
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02380
X-RAY DIFFRACTIONr_nbd_refined0.2050.2397
X-RAY DIFFRACTIONr_nbd_other0.1770.21817
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2930
X-RAY DIFFRACTIONr_nbtor_other0.080.21149
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2192
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.0850.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4420.234
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0570.21
X-RAY DIFFRACTIONr_mcbond_it0.6561.51591
X-RAY DIFFRACTIONr_mcbond_other0.1411.5530
X-RAY DIFFRACTIONr_mcangle_it0.85621981
X-RAY DIFFRACTIONr_scbond_it1.5153808
X-RAY DIFFRACTIONr_scangle_it2.1274.5629
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 87 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.020.05
TIGHT THERMAL0.140.5
LS refinement shellResolution: 1.65→1.695 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 40 -
Rwork0.247 741 -
all-781 -
obs-741 36.43 %

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