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- PDB-2fgh: ATP bound gelsolin -

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Basic information

Entry
Database: PDB / ID: 2fgh
TitleATP bound gelsolin
Componentsgelsolin
KeywordsCONTRACTILE PROTEIN / STRUCTURAL PROTEIN / gelsolin / ATP
Function / homology
Function and homology information


actin filament severing / barbed-end actin filament capping / actin polymerization or depolymerization / cell projection assembly / cilium assembly / phosphatidylinositol-4,5-bisphosphate binding / central nervous system development / actin filament binding / actin cytoskeleton / extracellular space ...actin filament severing / barbed-end actin filament capping / actin polymerization or depolymerization / cell projection assembly / cilium assembly / phosphatidylinositol-4,5-bisphosphate binding / central nervous system development / actin filament binding / actin cytoskeleton / extracellular space / metal ion binding / 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
ADENOSINE-5'-TRIPHOSPHATE / Gelsolin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMa, Q. / Robinson, R.C. / Burtnick, L.D. / Urosev, D.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The structure of gelsolin bound to ATP
Authors: Urosev, D. / Ma, Q. / Tan, A.L.C. / Robinson, R.C. / Burtnick, L.D.
History
DepositionDec 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2017Group: Data collection / Database references / Category: diffrn_source / pdbx_database_related / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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

Downloads & links

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Assembly

Deposited unit
A: gelsolin
B: gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,8584
Polymers161,8442
Non-polymers1,0142
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-13 kcal/mol
Surface area60540 Å2
MethodPISA
2
A: gelsolin
B: gelsolin
hetero molecules

A: gelsolin
B: gelsolin
hetero molecules

A: gelsolin
B: gelsolin
hetero molecules

A: gelsolin
B: gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)651,43216
Polymers647,3758
Non-polymers4,0578
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area31200 Å2
ΔGint-115 kcal/mol
Surface area227200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.344, 167.344, 149.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B
17A
27B
18A
28B
19A
29B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLYSLYSAA27 - 1353 - 111
21VALVALLYSLYSBB27 - 1353 - 111
12SERSERGLYGLYAA136 - 248112 - 224
22SERSERGLYGLYBB136 - 248112 - 224
13PROPROLYSLYSAA249 - 367225 - 343
23PROPROLYSLYSBB249 - 367225 - 343
14ASNASNVALVALAA368 - 393344 - 369
24ASNASNVALVALBB368 - 393344 - 369
15PROPROGLYGLYAA394 - 513370 - 489
25PROPROGLYGLYBB394 - 513370 - 489
16GLYGLYGLYGLYAA514 - 619490 - 595
26GLYGLYGLYGLYBB514 - 619490 - 595
17GLYGLYLEULEUAA620 - 734596 - 710
27GLYGLYLEULEUBB620 - 734596 - 710
18GLYGLYALAALAAA735 - 755711 - 731
28GLYGLYALAALABB735 - 755711 - 731
19ATPATPATPATPAC5380
29ATPATPATPATPBD9380

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
DetailsTHE BIOLOGICAL ASSEMBLY IS FROM A SINGLE POLYPEPTIDE CHAIN FOLDED INTO SIX STRUCTURALLY SIMIALAR DOMAINS, S1 THROUGH S6.

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Components

#1: Protein gelsolin / Actin-depolymerizing factor / ADF / Brevin


Mass: 80921.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: Q28372
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growMethod: vapor diffusion / pH: 8
Details: crystals were grown from drops containing a 1:1 ratio of 34% saturated ammonium sulfate solution, 100mM Tris-HCL reservoir solution, pH 8.0, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.957 Å
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.957 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 52123 / Num. obs: 52123 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 %
Reflection shellResolution: 2.8→2.9 Å / % possible all: 97

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.889 / SU B: 15.402 / SU ML: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.596 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2650 5.1 %RANDOM
Rwork0.242 ---
all0.243 52123 --
obs0.243 52123 98.62 %-
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: 57.155 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11266 0 62 50 11378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02111600
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210260
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.95115734
X-RAY DIFFRACTIONr_angle_other_deg1.415323922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77751438
X-RAY DIFFRACTIONr_chiral_restr0.0740.21668
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213058
X-RAY DIFFRACTIONr_gen_planes_other0.0110.022376
X-RAY DIFFRACTIONr_nbd_refined0.220.22328
X-RAY DIFFRACTIONr_nbd_other0.2520.211434
X-RAY DIFFRACTIONr_nbtor_other0.0870.26754
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2201
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.23
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT POSITIONAL / Weight position: 0.05

Ens-IDNumberRms dev position (Å)
116730.09
217050.06
316710.02
43940.06
517140.05
615000.01
717880.04
83100.02
9390.03
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.389 198
Rwork0.372 3471
obs-3669

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