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- PDB-1i8m: CRYSTAL STRUCTURE OF A RECOMBINANT ANTI-SINGLE-STRANDED DNA ANTIB... -

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Basic information

Entry
Database: PDB / ID: 1i8m
TitleCRYSTAL STRUCTURE OF A RECOMBINANT ANTI-SINGLE-STRANDED DNA ANTIBODY FRAGMENT COMPLEXED WITH DT5
Components
  • 5'-D(*TP*TP*TP*TP*T)-3'
  • 5'-D(P*TP*T)-3'
  • ANTIBODY HEAVY CHAIN FAB
  • ANTIBODY LIGHT CHAIN FAB
KeywordsIMMUNE SYSTEM/DNA / fab / antibody / anti-DNA antibody / autoantibody / lupus / IMMUNE SYSTEM-DNA COMPLEX
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / blood microparticle / immune response / extracellular space
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / : / DNA / Anti-colorectal carcinoma light chain / VH186.2-D-J-C mu protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTanner, J.J. / Komissarov, A.A. / Deutscher, S.L.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of an Antigen-Binding Fragment Bound to Single-Stranded DNA
Authors: Tanner, J.J. / Komissarov, A.A. / Deutscher, S.L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Molecular Replacement Studies of a Recombinant Antigen-Binding Fragment Complexed with Single-stranded DNA.
Authors: Prewitt, S.P. / Komissarov, A.A. / Deutscher, S.L. / Tanner, J.J.
History
DepositionMar 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2001Provider: 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 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _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
T: 5'-D(*TP*TP*TP*TP*T)-3'
D: 5'-D(P*TP*T)-3'
L: ANTIBODY LIGHT CHAIN FAB
H: ANTIBODY HEAVY CHAIN FAB
A: ANTIBODY LIGHT CHAIN FAB
B: ANTIBODY HEAVY CHAIN FAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,6747
Polymers97,5786
Non-polymers961
Water6,107339
1
T: 5'-D(*TP*TP*TP*TP*T)-3'
L: ANTIBODY LIGHT CHAIN FAB
H: ANTIBODY HEAVY CHAIN FAB


Theoretical massNumber of molelcules
Total (without water)49,2453
Polymers49,2453
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 5'-D(P*TP*T)-3'
A: ANTIBODY LIGHT CHAIN FAB
B: ANTIBODY HEAVY CHAIN FAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4294
Polymers48,3333
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.840, 171.840, 144.568
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is an antigen binding fragment, Fab. There are two Fabs in the asymmetric unit.

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Components

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DNA chain , 2 types, 2 molecules TD

#1: DNA chain 5'-D(*TP*TP*TP*TP*T)-3'


Mass: 1476.007 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*TP*T)-3'


Mass: 563.428 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Antibody , 2 types, 4 molecules LAHB

#3: Antibody ANTIBODY LIGHT CHAIN FAB / ANTI-SINGLE-STRANDED DNA ANTIGEN-BINDING FAB FRAGMENT


Mass: 23616.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PCOMB3/6-HIS / Production host: Escherichia coli (E. coli) / Strain (production host): DH12S / References: GenBank: 498315, UniProt: Q7TS98*PLUS
#4: Antibody ANTIBODY HEAVY CHAIN FAB / ANTI-SINGLE-STRANDED DNA ANTIGEN-BINDING FAB FRAGMENT


Mass: 24153.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PCOMB3/6-HIS / Production host: Escherichia coli (E. coli) / Strain (production host): DH12S / References: GenBank: 3399661, UniProt: Q924Q6*PLUS

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Non-polymers , 2 types, 340 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2 M ammonium sulfate, 0.1 M sodium acetate, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2sodium acetate11
Crystal grow
*PLUS
Temperature: 22 ℃ / PH range low: 5.2 / PH range high: 4.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 mg/mlDNA-11drop
25 MdT51dropexcess
30.1 Msodium acetate1reservoir
41.8-2.0 Mammonium sulfate1reservoirpH4.8-5.2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11731
21731
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X8C10.979
SYNCHROTRONNSLS X12B20.978
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDSep 21, 1999
ADSC QUANTUM 42CCDMar 23, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1NSLS X8C beamline opticsSINGLE WAVELENGTHMx-ray1
2NSLS X12B beamline opticsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9781
ReflectionResolution: 2.1→28 Å / Num. all: 72520 / Num. obs: 72520 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 19.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 3.6 / % possible all: 96
Reflection
*PLUS
Lowest resolution: 28 Å / % possible obs: 98.8 % / Num. measured all: 489562
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 95.9 %

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
AMoREphasing
X-PLORmodel building
CNS1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mlc

1mlc


Resolution: 2.1→27.66 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3972329.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 7190 9.9 %RANDOM
Rwork0.2203 ---
all0.229 72520 --
obs0.2203 72520 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.21 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.79 Å21.06 Å20 Å2
2--3.79 Å20 Å2
3----7.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→27.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6414 121 5 339 6879
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011155
X-RAY DIFFRACTIONc_angle_deg1.62386
X-RAY DIFFRACTIONc_dihedral_angle_d27.37438
X-RAY DIFFRACTIONc_improper_angle_d0.99896
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3023 1082 9.3 %
Rwork0.2725 10614 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.37438
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99896
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.304 / % reflection Rfree: 9.3 % / Rfactor obs: 0.274

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