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- PDB-1p5s: STRUCTURE AND FUNCTION OF THE CALPONIN-HOMOLOGY DOMAIN OF AN IQGA... -

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Basic information

Entry
Database: PDB / ID: 1p5s
TitleSTRUCTURE AND FUNCTION OF THE CALPONIN-HOMOLOGY DOMAIN OF AN IQGAP PROTEIN FROM SCHIZOSACCHAROMYCES POMBE
ComponentsRas GTPase-activating-like protein rng2
KeywordsCYTOKINE / Alpha-helical 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
: / Ras GTPase-activating-like protein rng2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Sulfur SAD / Resolution: 2.22 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 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 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 / 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.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.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _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: Ras GTPase-activating-like protein rng2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4305
Polymers22,6281
Non-polymers8024
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.884, 68.666, 35.309
Angle α, β, γ (deg.)90.00, 102.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ras GTPase-activating-like protein rng2 / Ring assembly protein 2


Mass: 22627.898 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-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 1.8 Å3/Da / Density % sol: 31.06 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.653 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2002 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.653 Å / Relative weight: 1
ReflectionResolution: 2.21→20.6 Å / Num. all: 6890 / Num. obs: 6890 / % possible obs: 97.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 16.45 %
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 8.72 % / Num. unique all: 570 / % possible all: 81.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: Sulfur SAD / Resolution: 2.22→21 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.862 / SU B: 5.556 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R: 0.57 / ESU R Free: 0.261
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.246 319 4.6 %RANDOM
Rwork0.19709 ---
all0.19921 6890 --
obs0.19921 6571 95.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.802 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.31 Å2
2---0.21 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.22→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 0 4 145 1452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221276
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.9731682
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.7425143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02908
X-RAY DIFFRACTIONr_gen_planes_other0.0130.023
X-RAY DIFFRACTIONr_nbd_refined0.3510.2718
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2108
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.5735753
X-RAY DIFFRACTIONr_mcangle_it3.66361194
X-RAY DIFFRACTIONr_scbond_it4.0526523
X-RAY DIFFRACTIONr_scangle_it5.8817.5488
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.216→2.273 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.302 12
Rwork0.231 351

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