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- PDB-1xf3: Structure of ligand-free Fab DNA-1 in space group P65 -

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Basic information

Entry
Database: PDB / ID: 1xf3
TitleStructure of ligand-free Fab DNA-1 in space group P65
Components
  • Fab Light chain
  • Fab heavy chain
KeywordsIMMUNE SYSTEM / antibody / Fab / immunoglobulin / anti-DNA / anti-ssDNA / autoantibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSchuermann, J.P. / Prewitt, S.P. / Deutscher, S.L. / Tanner, J.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Evidence for Structural Plasticity of Heavy Chain Complementarity-determining Region 3 in Antibody-ssDNA Recognition
Authors: Schuermann, J.P. / Prewitt, S.P. / Davies, C. / Deutscher, S.L. / Tanner, J.J.
History
DepositionSep 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab Light chain
H: Fab heavy chain
A: Fab Light chain
B: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)97,1964
Polymers97,1964
Non-polymers00
Water1,18966
1
L: Fab Light chain
H: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)48,5982
Polymers48,5982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-24 kcal/mol
Surface area19930 Å2
MethodPISA
2
A: Fab Light chain
B: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)48,5982
Polymers48,5982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-25 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.751, 201.751, 44.781
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe biological assembly is the Fab, which has one light chain and one heavy chain

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Components

#1: Antibody Fab Light chain


Mass: 23616.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: GenBank: 498315
#2: Antibody Fab heavy chain


Mass: 24982.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: GenBank: 3399661
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: isopropanol, PEG 4000, sodium citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2001
RadiationMonochromator: beamline optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.3→48.5 Å / Num. all: 46702 / Num. obs: 46702 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 16
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.455 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I8M

1i8m


Resolution: 2.3→48.5 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.951 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.288 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24259 2323 5 %RANDOM
Rwork0.20791 ---
all0.20963 46702 --
obs0.20963 44367 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.652 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20.29 Å20 Å2
2--0.58 Å20 Å2
3----0.88 Å2
Refine analyzeLuzzati sigma a free: 0.17 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6391 0 0 66 6457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216554
X-RAY DIFFRACTIONr_bond_other_d0.0040.025613
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9498938
X-RAY DIFFRACTIONr_angle_other_deg0.805313146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5535854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.21012
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027325
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021249
X-RAY DIFFRACTIONr_nbd_refined0.1780.2938
X-RAY DIFFRACTIONr_nbd_other0.2290.26066
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.23945
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2124
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1770.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.4641.54272
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87526885
X-RAY DIFFRACTIONr_scbond_it1.19332282
X-RAY DIFFRACTIONr_scangle_it1.9344.52053
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.325 154
Rwork0.296 3066
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)
16.14533.5331-1.27329.006-3.43953.29220.828-0.8813-0.8260.283-1.2303-1.6024-0.40790.43760.40230.2887-0.161-0.06620.27330.31960.674948.366170.502-35.794
22.3626-0.6237-0.69192.71190.72412.7292-0.0986-0.1388-0.04980.12830.16990.17650.2057-0.0078-0.07140.3993-0.0134-0.02230.32370.06690.262926.32294.80413.484
35.38240.32660.60665.06950.67732.92310.37491.31950.3192-0.1871-0.6087-0.65160.28860.58840.23380.17310.28320.08920.72060.35480.417452.562134.535-33.444
41.75460.511-1.05786.0391-5.351510.18750.01830.20010.0721-0.27180.63931.23950.1924-1.1005-0.65760.2047-0.0258-0.05660.31770.11150.582114.415121.913-6.511
58.13310.775-2.659121.8112-4.63364.21290.9308-0.48311.20281.3158-0.65071.7281-0.42190.0003-0.28010.2802-0.06450.08130.1893-0.04080.445227.41164.544-32.055
62.4951-0.48820.97983.4694-0.96724.37160.1595-0.0551-0.1398-0.011-0.0297-0.24330.25710.1951-0.12990.33780.0273-0.02140.31310.02260.289241.66994.895-2.799
77.7302-3.00412.12973.1391-1.55711.81750.0660.38040.2785-0.0516-0.2825-0.22040.07070.31290.21650.25220.05540.00140.33520.18360.404345.839136.308-18.922
82.3192-1.4839-1.01455.77150.9852.22080.0030.02880.17170.001-0.06690.06070.0026-0.05980.06380.2770.02460.00640.26040.04220.387429.09128.124-5.83
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA1 - 1081 - 108
2X-RAY DIFFRACTION2AC1 - 1081 - 108
3X-RAY DIFFRACTION3LA109 - 213109 - 213
4X-RAY DIFFRACTION4AC109 - 213109 - 213
5X-RAY DIFFRACTION5HB3 - 1133 - 120
6X-RAY DIFFRACTION6BD1 - 1131 - 120
7X-RAY DIFFRACTION7HB114 - 215121 - 222
8X-RAY DIFFRACTION8BD114 - 215121 - 222

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