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- PDB-1jhw: Ca2+-binding Mimicry in the Crystal Structure of the Eu3+-Bound M... -

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Basic information

Entry
Database: PDB / ID: 1jhw
TitleCa2+-binding Mimicry in the Crystal Structure of the Eu3+-Bound Mutant Human Macrophage Capping Protein Cap G
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 / actin polymerization or depolymerization / cell projection assembly / 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 / actin polymerization or depolymerization / cell projection assembly / Flemming body / ruffle / phosphatidylinositol-4,5-bisphosphate binding / centriole / central nervous system development / mitotic spindle / actin filament binding / actin cytoskeleton / melanosome / lamellipodium / protein-containing complex assembly / cadherin binding / protein domain specific binding / 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
EUROPIUM (III) ION / Macrophage-capping protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVorobiev, S.M. / Southwick, F.S. / Almo, S.C.
Citation
Journal: To be Published
Title: Crystal Structure of Mutant Human Macrophage Capping Protein
Authors: Vorobiev, S.M. / Southwick, F.S. / 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
DepositionJun 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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_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

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Assembly

Deposited unit
A: MACROPHAGE CAPPING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8713
Polymers38,5671
Non-polymers3042
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MACROPHAGE CAPPING PROTEIN
hetero molecules

A: MACROPHAGE CAPPING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7436
Polymers77,1352
Non-polymers6084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area6830 Å2
ΔGint-59 kcal/mol
Surface area30750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)205.596, 205.596, 56.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

21A-528-

HOH

31A-551-

HOH

41A-565-

HOH

51A-579-

HOH

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Components

#1: Protein MACROPHAGE CAPPING PROTEIN / ACTIN-REGULATORY PROTEIN CAP-G


Mass: 38567.375 Da / Num. of mol.: 1
Mutation: 83HLNTLLGE -> 83QLDDYLGG, 124AFHKTSTGAPAAIKK -> 124GFKHVVPNSVVVQR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P40121
#2: Chemical ChemComp-EU3 / EUROPIUM (III) ION


Mass: 151.964 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Eu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 4.46 Å3/Da / Density % sol: 72.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4.0 AMMONIUM FORMATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20-22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMimidazole HCl1drop
20.25 mMEGTA1drop
30.1 mM1dropMgCl2
41 mMdithiothreitol1drop
58-10 mg/mlprotein1drop
63.0-4.0 Mammonium formate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 21, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. all: 17298 / Num. obs: 17298 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 23.1
Reflection shellResolution: 2.79→2.9 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.328 / Num. unique all: 1938 / % possible all: 98
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 25 Å / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
Highest resolution: 2.8 Å / % possible obs: 98 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 6.66

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J72

1j72


Resolution: 2.8→24.73 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1963110.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 643 3.9 %RANDOM
Rwork0.248 ---
obs0.248 16517 92.8 %-
all-16517 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.23 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso mean: 75.4 Å2
Baniso -1Baniso -2Baniso -3
1-7.94 Å27.66 Å20 Å2
2--7.94 Å20 Å2
3----15.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 2.8→24.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 2 91 2529
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
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_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.131.5
X-RAY DIFFRACTIONc_mcangle_it9.372
X-RAY DIFFRACTIONc_scbond_it7.682
X-RAY DIFFRACTIONc_scangle_it10.812.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.428 107 4 %
Rwork0.413 2596 -
obs--93.1 %
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 25 Å / Rfactor obs: 0.248 / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04
LS refinement shell
*PLUS
Lowest resolution: 2.9 Å / Rfactor Rfree: 0.428 / Rfactor Rwork: 0.413

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