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- PDB-1ohq: Crystal structure of HEL4, a soluble human VH antibody domain res... -

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Basic information

Entry
Database: PDB / ID: 1ohq
TitleCrystal structure of HEL4, a soluble human VH antibody domain resistant to aggregation
ComponentsIMMUNOGLOBULIN
KeywordsIMMUNOGLOBULIN / ANTIBODY / IMMUNE SYSTEM / FV FRAGMENT / HEL4
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / immunoglobulin complex / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / immunoglobulin complex / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / Potential therapeutics for SARS / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy variable 3-23
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJespers, L. / Schon, O. / James, L.C. / Veprintsev, D. / Winter, G.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of Hel4, a Soluble, Refoldable Human V(H) Single Domain with a Germ-Line Scaffold
Authors: Jespers, L. / Schon, O. / James, L.C. / Veprintsev, D. / Winter, G.
History
DepositionMay 30, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMMUNOGLOBULIN
B: IMMUNOGLOBULIN


Theoretical massNumber of molelcules
Total (without water)25,7192
Polymers25,7192
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.121, 76.121, 187.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-2023-

HOH

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Components

#1: Antibody IMMUNOGLOBULIN


Mass: 12859.264 Da / Num. of mol.: 2 / Fragment: FV FRAGMENT, RESIDUES 1-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P01764*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
122.3 mg/mlprotein1drop
20.1 MHEPES1reservoirpH7.2
31.6 M1reservoirMgSO4
46 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.9793
DetectorDate: Sep 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→70 Å / Num. obs: 19067 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 4.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 6 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 99.7 % / Redundancy: 7 % / Rmerge(I) obs: 0.143
Reflection shell
*PLUS
% possible obs: 96 % / Redundancy: 6 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FGV

1fgv


Resolution: 2→70 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.26 -5 %
Rwork0.182 --
obs0.182 19067 99 %
Refinement stepCycle: LAST / Resolution: 2→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 0 183 1956
Refinement
*PLUS
Rfactor Rfree: 0.256 / Rfactor Rwork: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.007
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.259 / Rfactor Rwork: 0.183

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