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- PDB-2gsi: Crystal Structure of a Murine Fab in Complex with an 11 Residue P... -

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Basic information

Entry
Database: PDB / ID: 2gsi
TitleCrystal Structure of a Murine Fab in Complex with an 11 Residue Peptide Derived from Staphylococcal Nuclease
Components
  • Immunoglobulin (gamma) heavy chain (VH + CH1 fragment)
  • Immunoglobulin (kappa) light chain
  • ThermonucleaseMicrococcal nuclease
KeywordsIMMUNE SYSTEM / FAB / IGG / STAPHYLOCOCCAL NUCLEASE
Function / homology
Function and homology information


endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / membrane / metal ion binding
Similarity search - Function
Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / Immunoglobulin V-Type / Immunoglobulin V-set domain ...Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / 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
Thermonuclease / Igh protein / Thermonuclease
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsArmstrong, A.A. / Amzel, L.M.
CitationJournal: To be Published
Title: Crystal Structure of a Murine Fab in Complex with an 11 Residue Peptide Derived from Staphylococcal Nuclease
Authors: Armstrong, A.A. / Amzel, L.M.
History
DepositionApr 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 5, 2011Group: Derived calculations
Revision 1.4Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.5Aug 30, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Immunoglobulin (kappa) light chain
B: Immunoglobulin (gamma) heavy chain (VH + CH1 fragment)
C: Immunoglobulin (kappa) light chain
D: Immunoglobulin (gamma) heavy chain (VH + CH1 fragment)
E: Immunoglobulin (kappa) light chain
F: Immunoglobulin (gamma) heavy chain (VH + CH1 fragment)
G: Immunoglobulin (kappa) light chain
H: Immunoglobulin (gamma) heavy chain (VH + CH1 fragment)
X: Thermonuclease
Z: Thermonuclease
W: Thermonuclease
Y: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,53319
Polymers194,37212
Non-polymers1617
Water1,11762
1
A: Immunoglobulin (kappa) light chain
B: Immunoglobulin (gamma) heavy chain (VH + CH1 fragment)
W: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6395
Polymers48,5933
Non-polymers462
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-43 kcal/mol
Surface area19570 Å2
MethodPISA
2
C: Immunoglobulin (kappa) light chain
D: Immunoglobulin (gamma) heavy chain (VH + CH1 fragment)
X: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6164
Polymers48,5933
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-37 kcal/mol
Surface area20080 Å2
MethodPISA
3
E: Immunoglobulin (kappa) light chain
F: Immunoglobulin (gamma) heavy chain (VH + CH1 fragment)
Y: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6395
Polymers48,5933
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-51 kcal/mol
Surface area19640 Å2
MethodPISA
4
G: Immunoglobulin (kappa) light chain
H: Immunoglobulin (gamma) heavy chain (VH + CH1 fragment)
Z: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6395
Polymers48,5933
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-50 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.739, 131.040, 291.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsChain A, Chain B, Chain W form an intact Fab with liganded peptide / Chain C, Chain D, Chain X form an intact Fab with liganded peptide / Chain E, Chain F, Chain Y form an intact Fab with liganded peptide / Chain G, Chain H, Chain Z form an intact Fab with liganded peptide

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Components

#1: Antibody
Immunoglobulin (kappa) light chain


Mass: 23483.934 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Ascites / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c
#2: Antibody
Immunoglobulin (gamma) heavy chain (VH + CH1 fragment)


Mass: 23789.611 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Ascites / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c / References: UniProt: Q6PF95
#3: Protein/peptide
Thermonuclease / Micrococcal nuclease / TNase / Micrococcal nuclease / Staphylococcal nuclease


Mass: 1319.570 Da / Num. of mol.: 4 / Fragment: Residues: 123-133 / Source method: obtained synthetically / Details: Peptide synthesized using standard Fmoc chemistry
References: UniProt: Q8NXI6, UniProt: P00644*PLUS, micrococcal nuclease
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 18% PEG 2000, 16% isopropanol, 0.1 M sodium citrate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2004 / Details: Pt coated toroidal Si mirror
RadiationMonochromator: Double flat Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 42035 / Num. obs: 42035 / % possible obs: 84.6 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 24.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.489 / % possible all: 83.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries: 1f11, 2aju, 1f58, 1cr9

1f11

2aju

1f58

1cr9


Resolution: 2.81→48.74 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.833 / SU B: 41.797 / SU ML: 0.379 / Cross valid method: THROUGHOUT / ESU R Free: 0.514 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29278 2175 5.2 %RANDOM
Rwork0.22074 ---
obs0.22451 39809 84.25 %-
all-41984 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.415 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.81→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13309 0 7 62 13378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213686
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.95518678
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.09551733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30324.58524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.904152171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0221550
X-RAY DIFFRACTIONr_chiral_restr0.0960.22130
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210284
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2570.25836
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.29020
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2524
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3380.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6461.58924
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.136214233
X-RAY DIFFRACTIONr_scbond_it1.61635505
X-RAY DIFFRACTIONr_scangle_it2.6414.54445
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.806→2.879 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 160 -
Rwork0.299 2758 -
obs--80.97 %

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