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- PDB-1p2x: CRYSTAL STRUCTURE OF THE CALPONIN-HOMOLOGY DOMAIN OF RNG2 FROM SC... -

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Basic information

Entry
Database: PDB / ID: 1p2x
TitleCRYSTAL STRUCTURE OF THE CALPONIN-HOMOLOGY DOMAIN OF RNG2 FROM SCHIZOSACCHAROMYCES POMBE
ComponentsRas GTPase-activating-like protein
KeywordsPROTEIN BINDING / 4 HELICES / BUNDLE
Function / homology
Function and homology information


actomyosin contractile ring assembly actin filament bundle convergence / RHOV GTPase cycle / RHOA GTPase cycle / RHO GTPases activate IQGAPs / medial cortical node / mitotic actomyosin contractile ring, proximal layer / mitotic actomyosin contractile ring assembly actin filament organization / RHOQ GTPase cycle / RHOU GTPase cycle / Neutrophil degranulation ...actomyosin contractile ring assembly actin filament bundle convergence / RHOV GTPase cycle / RHOA GTPase cycle / RHO GTPases activate IQGAPs / medial cortical node / mitotic actomyosin contractile ring, proximal layer / mitotic actomyosin contractile ring assembly actin filament organization / RHOQ GTPase cycle / RHOU GTPase cycle / Neutrophil degranulation / mitotic actomyosin contractile ring assembly / mitotic spindle pole body / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring contraction / cytoskeletal anchor activity / spindle pole body / GTPase activator activity / actin filament binding / nuclear envelope / cell cortex / calmodulin binding / cytoplasm
Similarity search - Function
RasGAP protein, C-terminal / RasGAP C-terminus / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / IQ calmodulin-binding motif / Calponin homology domain ...RasGAP protein, C-terminal / RasGAP C-terminus / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / IQ calmodulin-binding motif / Calponin homology domain / Calponin homology (CH) domain / Rho GTPase activation protein / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / IQ motif profile. / IQ motif, EF-hand binding site / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / Ras GTPase-activating-like protein rng2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.21 Å
AuthorsWang, C.-H. / Balasubramanian, M.K. / Dokland, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure, crystal packing and molecular dynamics of the calponin-homology domain of Schizosaccharomyces pombe Rng2.
Authors: Wang, C.H. / Balasubramanian, M.K. / Dokland, T.
History
DepositionApr 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Ras GTPase-activating-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,35512
Polymers18,4761
Non-polymers87911
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.226, 68.836, 39.811
Angle α, β, γ (deg.)90.00, 105.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ras GTPase-activating-like protein / Rng2 protein


Mass: 18476.211 Da / Num. of mol.: 1 / Fragment: CALPONIN-HOMOLOGY DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: RNG2 OR SPAC4F8.13C / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: O14188
#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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 Å3/Da / Density % sol: 38.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 21% PEG 3000, 0.3M Calcium Acetate, 0.1M Tris pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.919087, 0.919338, 0.855057
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2002 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9190871
20.9193381
30.8550571
ReflectionResolution: 2.21→22.65 Å / Num. obs: 7532 / % possible obs: 89.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.47 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 0.053
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 2.09 % / Rmerge(I) obs: 0.077 / Mean I/σ(I) obs: 9.39 / Num. unique all: 202 / Rsym value: 0.077 / % possible all: 24.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.21→22.65 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 930480.25 / Data cutoff high rms absF: 930480.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 369 4.9 %RANDOM
Rwork0.206 ---
all0.208 ---
obs0.206 7347 92.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.4937 Å2 / ksol: 0.346508 e/Å3
Displacement parametersBiso mean: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20.55 Å2
2---2.4 Å20 Å2
3---2.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.21→22.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 0 11 157 1471
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_improper_angle_d1.01
LS refinement shellResolution: 2.21→2.35 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 42 4.7 %
Rwork0.235 852 -
obs-25342 66.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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