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- PDB-2x1q: Gelsolin Nanobody -

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Basic information

Entry
Database: PDB / ID: 2x1q
TitleGelsolin Nanobody
ComponentsGELSOLIN NANOBODY
KeywordsCONTRACTILE PROTEIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsVan Den Abbeele, A. / Declercq, S. / De Ganck, A. / De Corte, V. / Van Loo, B. / Srinivasan, V. / Steyaert, J. / Van De Kerckhove, J. / Gettemans, J.
CitationJournal: Cell.Mol.Life Sci. / Year: 2010
Title: A Llama-Derived Gelsolin Single-Domain Antibody Blocks Gelsolin-G-Actin Interaction.
Authors: Van Den Abbeele, A. / De Clercq, S. / De Ganck, A. / De Corte, V. / Van Loo, B. / Soror, S.H. / Srinivasan, V. / Steyaert, J. / Vandekerckhove, J. / Gettemans, J.
History
DepositionJan 3, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GELSOLIN NANOBODY
B: GELSOLIN NANOBODY


Theoretical massNumber of molelcules
Total (without water)27,8132
Polymers27,8132
Non-polymers00
Water8,053447
1
A: GELSOLIN NANOBODY


Theoretical massNumber of molelcules
Total (without water)13,9061
Polymers13,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GELSOLIN NANOBODY


Theoretical massNumber of molelcules
Total (without water)13,9061
Polymers13,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.908, 63.425, 50.010
Angle α, β, γ (deg.)90.00, 90.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody GELSOLIN NANOBODY


Mass: 13906.346 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAMA GLAMA (llama) / Production host: ESCHERICHIA COLI (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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

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Sample preparation

CrystalDensity Matthews: 1.76 Å3/Da / Density % sol: 29.48 % / Description: NONE
Crystal growDetails: 30% PEG 1000, 100 MM PHOSPHATE/ CITRATE PH 4.4, 100 MM LISO4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9834
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9834 Å / Relative weight: 1
ReflectionResolution: 1.06→20 Å / Num. obs: 92321 / % possible obs: 91.3 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.2
Reflection shellResolution: 1.06→1.1 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.78 / % possible all: 77.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKLdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HCV

1hcv


Resolution: 1.06→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.927 / SU B: 0.945 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 4617 5 %RANDOM
Rwork0.213 ---
obs0.214 87704 91.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.06 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.06→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 0 447 2299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221891
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.171.9412559
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64123.37189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1615293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8891514
X-RAY DIFFRACTIONr_chiral_restr0.0690.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021459
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.2875
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21314
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2344
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.276
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6631.51206
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97221869
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5993801
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1164.5690
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.06→1.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 273 -
Rwork0.238 5120 -
obs--72.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0867-0.44230.14381.02780.10540.4988-0.0438-0.03480.02510.02860.0179-0.0503-0.0023-0.00250.0259-0.05580.00220.0028-0.07140.0016-0.072919.68070.653249.0625
21.15620.4203-0.17690.85890.05820.5119-0.04210.043-0.017-0.03460.0181-0.04480.006-0.00810.024-0.0554-0.0031-0.0008-0.07180.0005-0.07011.6591-1.086725.8133
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 127
2X-RAY DIFFRACTION2B3 - 127

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