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- PDB-4m61: Crystal structure of unliganded anti-DNA Fab A52 -

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Basic information

Entry
Database: PDB / ID: 4m61
TitleCrystal structure of unliganded anti-DNA Fab A52
Components
  • Fab A52 heavy chain
  • Fab A52 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsStanfield, R.L. / Eilat, D. / Wilson, I.A.
CitationJournal: Proteins / Year: 2014
Title: Crystal structure determination of anti-DNA Fab A52.
Authors: Stanfield, R.L. / Eilat, D.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Aug 6, 2014Group: Database references
Revision 1.3Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Fab A52 light chain
B: Fab A52 heavy chain
C: Fab A52 light chain
D: Fab A52 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,14723
Polymers95,3224
Non-polymers1,82519
Water13,854769
1
A: Fab A52 light chain
B: Fab A52 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,62212
Polymers47,6612
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-94 kcal/mol
Surface area19830 Å2
MethodPISA
2
C: Fab A52 light chain
D: Fab A52 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,52511
Polymers47,6612
Non-polymers8659
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-157 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.784, 61.380, 121.223
Angle α, β, γ (deg.)90.00, 96.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab A52 light chain


Mass: 24150.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: NZB/NZW F1
#2: Antibody Fab A52 heavy chain


Mass: 23510.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: NZB/NZW F1
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 769 / 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: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.4 M ammonium sulfate, 0.07 M sodium citrate, 2% PEG400, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 28, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.62→43 Å / Num. all: 94152 / Num. obs: 94152 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 28.7
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4662 / % possible all: 95.4

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Processing

Software
NameVersionClassification
EPMRphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MRF

1mrf


Resolution: 1.62→21.694 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 24.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2323 9434 10.02 %
Rwork0.1919 --
obs0.1959 94118 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→21.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6690 0 95 769 7554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087114
X-RAY DIFFRACTIONf_angle_d1.1829725
X-RAY DIFFRACTIONf_dihedral_angle_d12.9182556
X-RAY DIFFRACTIONf_chiral_restr0.0841085
X-RAY DIFFRACTIONf_plane_restr0.0051218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.63840.3642970.35562781X-RAY DIFFRACTION95
1.6384-1.65770.3343130.28672877X-RAY DIFFRACTION97
1.6577-1.67790.31963300.25052796X-RAY DIFFRACTION97
1.6779-1.69910.3293130.25082837X-RAY DIFFRACTION96
1.6991-1.72150.29433370.25642782X-RAY DIFFRACTION97
1.7215-1.7450.27443270.23462800X-RAY DIFFRACTION96
1.745-1.770.29443320.23512779X-RAY DIFFRACTION96
1.77-1.79640.30813370.23832789X-RAY DIFFRACTION96
1.7964-1.82440.25513240.20972769X-RAY DIFFRACTION95
1.8244-1.85430.27292830.21442837X-RAY DIFFRACTION96
1.8543-1.88630.24923190.20682763X-RAY DIFFRACTION94
1.8863-1.92060.24742910.20582793X-RAY DIFFRACTION96
1.9206-1.95750.25893210.19342725X-RAY DIFFRACTION94
1.9575-1.99740.24272840.19782793X-RAY DIFFRACTION95
1.9974-2.04080.2332990.1932780X-RAY DIFFRACTION94
2.0408-2.08820.24523030.21072741X-RAY DIFFRACTION94
2.0882-2.14040.25023300.20412726X-RAY DIFFRACTION94
2.1404-2.19820.23873090.1882791X-RAY DIFFRACTION94
2.1982-2.26280.23023100.19152765X-RAY DIFFRACTION95
2.2628-2.33580.22632970.19082773X-RAY DIFFRACTION94
2.3358-2.41920.24493190.20292763X-RAY DIFFRACTION95
2.4192-2.51590.26523010.19582866X-RAY DIFFRACTION96
2.5159-2.63020.24913280.18942800X-RAY DIFFRACTION96
2.6302-2.76860.23023180.1922868X-RAY DIFFRACTION97
2.7686-2.94170.24373440.1982864X-RAY DIFFRACTION98
2.9417-3.16820.21653090.1912878X-RAY DIFFRACTION98
3.1682-3.48590.21563150.17212940X-RAY DIFFRACTION98
3.4859-3.98750.20793180.16452943X-RAY DIFFRACTION99
3.9875-5.01360.16773110.1453001X-RAY DIFFRACTION100
5.0136-21.69590.1963150.19153064X-RAY DIFFRACTION100

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