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- PDB-1nsn: THE CRYSTAL STRUCTURE OF ANTIBODY N10-STAPHYLOCOCCAL NUCLEASE COM... -

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Basic information

Entry
Database: PDB / ID: 1nsn
TitleTHE CRYSTAL STRUCTURE OF ANTIBODY N10-STAPHYLOCOCCAL NUCLEASE COMPLEX AT 2.9 ANGSTROMS RESOLUTION
Components
  • (IGG FAB (IGG1, KAPPA)) x 2
  • STAPHYLOCOCCAL NUCLEASE
KeywordsCOMPLEX (IMMUNOGLOBULIN/HYDROLASE) / IMMUNOGLOBULIN / STAPHYLOCOCCAL NUCLEASE / COMPLEX (IMMUNOGLOBULIN-HYDROLASE) COMPLEX
Function / homology
Function and homology information


3' overhang single-stranded DNA endodeoxyribonuclease activity / micrococcal nuclease / nucleic acid binding / extracellular region / metal ion binding / membrane
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsSheriff, S. / Bossart-Whitaker, P.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: The crystal structure of the antibody N10-staphylococcal nuclease complex at 2.9 A resolution.
Authors: Bossart-Whitaker, P. / Chang, C.Y. / Novotny, J. / Benjamin, D.C. / Sheriff, S.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Analysis of an Anti-Staphylococcal Nuclease-Staphylococcal Nuclease Complex and of a Second Anti-Staphylococcal Nuclease Antibody
Authors: Chang, C.Y. / Bossart-Whitaker, P. / Tabernero, L. / Einspahr, H. / Workman, L. / Benjamin, D.C. / Sheriff, S.
History
DepositionJun 6, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG FAB (IGG1, KAPPA)
H: IGG FAB (IGG1, KAPPA)
S: STAPHYLOCOCCAL NUCLEASE


Theoretical massNumber of molelcules
Total (without water)63,6133
Polymers63,6133
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)234.700, 43.500, 74.400
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 95 / 3: CIS PROLINE - PRO H 149 / 4: CIS PROLINE - PRO H 151 / 5: CIS PROLINE - PRO H 202 / 6: CIS PROLINE - PRO S 117

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Components

#1: Antibody IGG FAB (IGG1, KAPPA) / N10 FAB IMMUNOGLOBULIN


Mass: 24189.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: CAF1
#2: Antibody IGG FAB (IGG1, KAPPA) / N10 FAB IMMUNOGLOBULIN


Mass: 22580.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: CAF1 / References: GenBank: 1513182
#3: Protein STAPHYLOCOCCAL NUCLEASE / STAPHYLOCOCCAL NUCLEASE RIBONUCLEASE / (DEOXYRIBONUCLEASE)-3'-NUCLEOTIDOHYDROLASE


Mass: 16843.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: FOGGI / Gene: NUCLEASE / Plasmid: PFOG405 / Gene (production host): NUCLEASE / Production host: Escherichia coli (E. coli) / References: UniProt: P00644, micrococcal nuclease
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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Chang, C.Y., (1994) J.Mol.Biol., 239, 154.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMTris-maleic acid1reservoir
21.2 Msodium citrate1reservoir
39 mg/mlprotein1drop

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→38 Å / Num. obs: 14626 / % possible obs: 78.7 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.048
Reflection
*PLUS
% possible obs: 81 % / Num. measured all: 32555 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
Highest resolution: 2.77 Å / Lowest resolution: 2.89 Å / % possible obs: 25 % / Rmerge(I) obs: 0.103

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Processing

Software
NameVersionClassification
XENGENdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.8→5 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.195 --
obs0.195 11488 81 %
Displacement parametersBiso mean: 18 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 0 0 4390
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.9
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 5 Å / Rfactor Rfree: 0.284
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.9

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