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- PDB-2x1p: Gelsolin Nanobody -

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Basic information

Entry
Database: PDB / ID: 2x1p
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: 1.1 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 16, 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
C: GELSOLIN NANOBODY
D: GELSOLIN NANOBODY


Theoretical massNumber of molelcules
Total (without water)54,7204
Polymers54,7204
Non-polymers00
Water14,214789
1
A: GELSOLIN NANOBODY


Theoretical massNumber of molelcules
Total (without water)13,6801
Polymers13,6801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GELSOLIN NANOBODY


Theoretical massNumber of molelcules
Total (without water)13,6801
Polymers13,6801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GELSOLIN NANOBODY


Theoretical massNumber of molelcules
Total (without water)13,6801
Polymers13,6801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GELSOLIN NANOBODY


Theoretical massNumber of molelcules
Total (without water)13,6801
Polymers13,6801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.948, 59.342, 81.651
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 3 - 126 / Label seq-ID: 3 - 126

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Antibody
GELSOLIN NANOBODY


Mass: 13679.952 Da / Num. of mol.: 4
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.: 789 / 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: 2.24 Å3/Da / Density % sol: 50.34 % / 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: 1.1→19.75 Å / Num. obs: 204183 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.6
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.08 / % possible all: 99.8

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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: 1.1→19.51 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 0.817 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 10788 5 %RANDOM
Rwork0.203 ---
obs0.204 204182 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.1→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 0 789 4357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213636
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.9364916
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5995464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27123.636176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.70915560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1031532
X-RAY DIFFRACTIONr_chiral_restr0.0770.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022840
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21750
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22471
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0850.2680
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.2123
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.272
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7391.52357
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16123664
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.67431452
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5174.51252
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 674 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.410.5
2Bmedium positional0.330.5
3Cmedium positional0.390.5
4Dmedium positional0.330.5
1Amedium thermal0.622
2Bmedium thermal0.592
3Cmedium thermal0.592
4Dmedium thermal0.592
LS refinement shellResolution: 1.1→1.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 775 -
Rwork0.204 14785 -
obs--98.62 %
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)
10.2458-0.1014-0.02230.37860.15540.26820.01250.0436-0.02930.0217-0.0348-0.00110.0207-0.02620.0222-0.00540.00170.0003-0.0014-0.0062-0.005444.440847.845126.4587
20.2780.1180.00940.2864-0.18010.31490.0074-0.0396-0.0123-0.0359-0.01710.00880.02110.02070.0097-0.00640.00010.0016-0.00250.0016-0.008239.934977.53712.9631
30.2767-0.1002-0.01740.2813-0.18320.31230.00730.04030.01130.0357-0.01610.0106-0.02140.02040.0088-0.00580.0003-0.0018-0.00220.0018-0.008867.909259.720427.862
40.26040.08990.01730.3760.15430.25760.0121-0.04520.0286-0.0222-0.0335-0.0025-0.0213-0.02580.0214-0.0049-0.0017-0.0005-0.0015-0.0062-0.005972.414789.408114.3653
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 126
2X-RAY DIFFRACTION2B3 - 126
3X-RAY DIFFRACTION3C3 - 126
4X-RAY DIFFRACTION4D3 - 126

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