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- PDB-1j72: Crystal Structure of Mutant Macrophage Capping Protein (Cap G) wi... -

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Basic information

Entry
Database: PDB / ID: 1j72
TitleCrystal Structure of Mutant Macrophage Capping Protein (Cap G) with Actin-severing Activity in the Ca2+-Free Form
ComponentsMacrophage capping protein
KeywordsSTRUCTURAL PROTEIN / actin / human / capping / cap g / macrophage / gCap39 / Mbhl / gelsolin
Function / homology
Function and homology information


F-actin capping protein complex / actin filament severing / barbed-end actin filament capping / cell projection assembly / actin polymerization or depolymerization / Flemming body / ruffle / phosphatidylinositol-4,5-bisphosphate binding / centriole / central nervous system development ...F-actin capping protein complex / actin filament severing / barbed-end actin filament capping / cell projection assembly / actin polymerization or depolymerization / Flemming body / ruffle / phosphatidylinositol-4,5-bisphosphate binding / centriole / central nervous system development / actin filament binding / mitotic spindle / melanosome / lamellipodium / actin cytoskeleton / chromosome / protein-containing complex assembly / cadherin binding / protein domain specific binding / intracellular membrane-bounded organelle / protein-containing complex binding / nucleolus / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Macrophage-capping protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsVorobiev, S.M. / Southwick, F.S. / Storokopytov, B. / Almo, S.C.
Citation
Journal: To be Published
Title: Crystal Structure of Mutant Human Macrophage Capping Protein
Authors: Vorobiev, S.M. / Southwick, F.S. / Storokopytov, B. / Almo, S.C.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Gain-of-function mutations conferring actin-severing activity to human macrophage Cap G
Authors: Southwick, F.S.
History
DepositionMay 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage capping protein


Theoretical massNumber of molelcules
Total (without water)38,6251
Polymers38,6251
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Macrophage capping protein

A: Macrophage capping protein


Theoretical massNumber of molelcules
Total (without water)77,2512
Polymers77,2512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area5950 Å2
ΔGint-17 kcal/mol
Surface area31370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)206.623, 206.623, 56.174
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Macrophage capping protein / ACTIN-REGULATORY PROTEIN CAP-G


Mass: 38625.477 Da / Num. of mol.: 1
Mutation: 108HLNTLLGE -> 108QLDDYLGG; 148AFHTSTGAPAAIKK -> 148GFKHVVPNEVVVQR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40121
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 4.48 Å3/Da / Density % sol: 72.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Tris-HCl, pH 7.0-8.0, 3.5 - 4.0 ammonium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97178 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97178 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. all: 24873 / Num. obs: 24873 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.86 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.097
Reflection shellResolution: 2.5→2.53 Å / Redundancy: 3.54 % / Rmerge(I) obs: 0.431 / Num. unique all: 1051 / % possible all: 85.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
Rotptf_6Dmodel building
CNS1refinement
ROTPTFV. 6Dphasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→14.96 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2189205.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.299 862 3.8 %RANDOM
Rwork0.243 ---
obs0.243 22664 91.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.11 Å2 / ksol: 0.308 e/Å3
Displacement parametersBiso mean: 65.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.6 Å25.03 Å20 Å2
2--5.6 Å20 Å2
3----11.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 2.5→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 0 82 2588
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.171.5
X-RAY DIFFRACTIONc_mcangle_it10.552
X-RAY DIFFRACTIONc_scbond_it9.452
X-RAY DIFFRACTIONc_scangle_it12.652.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 107 3.5 %
Rwork0.402 2945 -
obs--75.3 %

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