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- PDB-1dql: CRYSTAL STRUCTURE OF AN UNLIGANDED (NATIVE) FV FROM A HUMAN IGM A... -

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Basic information

Entry
Database: PDB / ID: 1dql
TitleCRYSTAL STRUCTURE OF AN UNLIGANDED (NATIVE) FV FROM A HUMAN IGM ANTI-PEPTIDE ANTIBODY
Components(IGM MEZ IMMUNOGLOBULIN) x 2
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / ANTIBODY / IgM / Fv
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsRamsland, P.A. / Shan, L. / Moomaw, C.R. / Slaughter, C.A. / Guddat, L.W. / Edmundson, A.B.
CitationJournal: Mol.Immunol. / Year: 2000
Title: An unusual human IgM antibody with a protruding HCDR3 and high avidity for its peptide ligands.
Authors: Ramsland, P.A. / Shan, L. / Moomaw, C.R. / Slaughter, C.A. / Fan, Z. / Guddat, L.W. / Edmundson, A.B.
History
DepositionJan 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: IGM MEZ IMMUNOGLOBULIN
H: IGM MEZ IMMUNOGLOBULIN


Theoretical massNumber of molelcules
Total (without water)24,7422
Polymers24,7422
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-8 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.570, 61.130, 42.200
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe Mez Fv is a non-covalent heterodimer of VL (chain L) and VH (chain H)

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Components

#1: Antibody IGM MEZ IMMUNOGLOBULIN


Mass: 11527.743 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN VARIABLE DOMAIN FRAGMENT / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody IGM MEZ IMMUNOGLOBULIN


Mass: 13214.604 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN VARIABLE DOMAIN FRAGMENT / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.72 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 295 K / Method: microseeding, sitting drop / pH: 7
Details: 6-8% (W/V) PEG 8000, 0.05% (W/V) SODIUM AZIDE, pH 7.0, MICROSEEDING, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
145-50 mg/mlprotein11
20.05 %(w/v)sodium azide11
36-8 %(w/v)PEG800011

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 19, 1990
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.58→20 Å / Num. all: 7111 / Num. obs: 7111 / % possible obs: 84.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.25 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 12.4
Reflection shellResolution: 2.58→2.75 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.167 / % possible all: 40
Reflection
*PLUS
Highest resolution: 2.6 Å / % possible obs: 83.4 %
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.76 Å / % possible obs: 40.6 %

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
CNSrefinement
RefinementResolution: 2.6→20 Å / Rfactor Rfree error: 0.009 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.261 764 11 %RANDOM
Rwork0.181 ---
all0.191 6963 --
obs0.191 6963 83.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.31 Å2 / ksol: 0.252 e/Å3
Displacement parametersBiso mean: 18.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 0 18 1758
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.35
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 65 11.5 %
Rwork0.286 502 -
obs--40.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2pca.parpca.top
X-RAY DIFFRACTION3water_rep.param
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d27.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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