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- PDB-1xf4: Structure of ligand-free Fab DNA-1 in space group P321 solved fro... -

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Basic information

Entry
Database: PDB / ID: 1xf4
TitleStructure of ligand-free Fab DNA-1 in space group P321 solved from crystals with perfect hemihedral twinning
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
KeywordsIMMUNE SYSTEM / antibody / Fab / immunoglobulin / anti-DNA / anti-ssDNA / autoantibody / twinning
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / Derived calculations / 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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
L: Fab light chain
H: Fab heavy chain
A: Fab light chain
B: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4847
Polymers97,1964
Non-polymers2883
Water63135
1
L: Fab light chain
H: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7904
Polymers48,5982
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-23 kcal/mol
Surface area19300 Å2
MethodPISA
2
A: Fab light chain
B: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6943
Polymers48,5982
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-24 kcal/mol
Surface area19170 Å2
MethodPISA
3
L: Fab light chain
H: Fab heavy chain
hetero molecules

L: Fab light chain
H: Fab heavy chain
hetero molecules

L: Fab light chain
H: Fab heavy chain
hetero molecules

A: Fab light chain
B: Fab heavy chain
hetero molecules

A: Fab light chain
B: Fab heavy chain
hetero molecules

A: Fab light chain
B: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,45321
Polymers291,58912
Non-polymers8659
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_654-y+1,x-y,z-11
crystal symmetry operation3_664-x+y+1,-x+1,z-11
Buried area32710 Å2
ΔGint-390 kcal/mol
Surface area103780 Å2
MethodPISA
4
A: Fab light chain
B: Fab heavy chain
hetero molecules

A: Fab light chain
B: Fab heavy chain
hetero molecules

A: Fab light chain
B: Fab heavy chain
hetero molecules

L: Fab light chain
H: Fab heavy chain
hetero molecules

L: Fab light chain
H: Fab heavy chain
hetero molecules

L: Fab light chain
H: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,45321
Polymers291,58912
Non-polymers8659
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_656-y+1,x-y,z+11
crystal symmetry operation3_666-x+y+1,-x+1,z+11
Buried area31190 Å2
ΔGint-264 kcal/mol
Surface area104170 Å2
MethodPISA
5
L: Fab light chain
H: Fab heavy chain
hetero molecules

L: Fab light chain
H: Fab heavy chain
hetero molecules

L: Fab light chain
H: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,37112
Polymers145,7946
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area11850 Å2
ΔGint-197 kcal/mol
Surface area56800 Å2
MethodPISA
6
A: Fab light chain
B: Fab heavy chain
hetero molecules

A: Fab light chain
B: Fab heavy chain
hetero molecules

A: Fab light chain
B: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,0829
Polymers145,7946
Non-polymers2883
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area11470 Å2
ΔGint-160 kcal/mol
Surface area56360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.179, 179.179, 91.985
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11L-301-

SO4

21L-301-

SO4

31L-302-

SO4

41L-302-

SO4

51A-303-

SO4

61A-303-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21A
12L
22A
13H
23B
14H
24B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUARGARGLA1 - 1081 - 108
21GLUGLUARGARGAC1 - 1081 - 108
12ALAALAGLUGLULA109 - 213109 - 213
22ALAALAGLUGLUAC109 - 213109 - 213
13GLNGLNSERSERHB1 - 1131 - 120
23GLNGLNSERSERBD1 - 1131 - 120
14ALAALAARGARGHB114 - 213121 - 220
24ALAALAARGARGBD114 - 213121 - 220

NCS ensembles :
ID
1
2
3
4
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 / Fragment antigen-binding


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 / Fragment antigen-binding


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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 1

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Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.9
Details: ammonium sulfate, sodium acetate, pH 4.9, 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: 2.5→49.5 Å / Num. all: 54454 / Num. obs: 54454 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 13
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.511 / % possible all: 81

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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: 2.5→49.5 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.709 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.327 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22398 4384 9.6 %RANDOM
Rwork0.18303 ---
all0.18696 51454 --
obs0.18696 41498 77.8 %-
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: 23.847 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.15 Å20 Å2
2---0.29 Å20 Å2
3---0.44 Å2
Refine analyzeLuzzati sigma a free: 0.18 Å
Refinement stepCycle: LAST / Resolution: 2.5→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6360 0 15 35 6410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216537
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9498916
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0665846
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_restr0.0960.21012
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024873
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.22716
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.531.54240
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97326851
X-RAY DIFFRACTIONr_scbond_it1.51232297
X-RAY DIFFRACTIONr_scangle_it2.3154.52065
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 2 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A787medium positional0.120.5
2A820medium positional0.140.5
3B869medium positional0.40.5
4B683medium positional0.130.5
1A787medium thermal0.672
2A820medium thermal0.612
3B869medium thermal0.592
4B683medium thermal0.642
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.261 264
Rwork0.21 2621
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)
11.2299-0.52650.25841.76480.57124.0387-0.0623-0.44670.06470.30150.0825-0.02930.05890.1151-0.02020.01380.02740.02310.10380.02340.11381.75164.73118.126
21.37920.06990.57241.480.54374.63170.05450.45050.0107-0.3499-0.0117-0.02920.17780.1624-0.04270.03460.05020.0230.07310.03070.099174.34952.67970.028
32.6152-2.25440.30374.7414-0.19221.20620.19250.42190.6171-0.3-0.1737-0.4312-0.49120.0142-0.01880.1190.02220.09270.10830.06230.225276.39686.334-12.604
46.4218-0.3389-0.28071.46410.39040.6414-0.193-0.5888-0.64540.23370.16490.37940.2606-0.38740.02810.07190.01480.02340.17130.09870.193652.77447.274100.702
52.47970.5887-1.2792.2199-1.21124.9529-0.0854-0.17210.06270.29540.0527-0.0133-0.2013-0.12350.03260.11170.060.00240.2173-0.02120.127367.38279.33227.441
61.35590.1925-0.29083.2407-1.77735.38760.01940.3247-0.0046-0.15260.05190.00280.017-0.3769-0.07140.1020.0514-0.02350.24180.02360.105454.86458.6760.869
72.0825-0.2682-0.43592.4360.98693.51330.03880.24480.0648-0.2530.00770.0124-0.3164-0.1466-0.04650.04310.05210.03590.14470.05550.163261.62483.621-5.936
82.635-0.0364-0.04942.29080.35864.3593-0.0174-0.09940.20550.0971-0.06110.0367-0.0554-0.61480.07850.06720.10120.0170.20760.04680.163948.25561.8793.978
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 DIFFRACTION5HB1 - 1131 - 120
6X-RAY DIFFRACTION6BD1 - 1131 - 120
7X-RAY DIFFRACTION7HB114 - 213121 - 220
8X-RAY DIFFRACTION8BD114 - 213121 - 220

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