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- PDB-1ngp: N1G9 (IGG1-LAMBDA) FAB FRAGMENT COMPLEXED WITH (4-HYDROXY-3-NITRO... -

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Basic information

Entry
Database: PDB / ID: 1ngp
TitleN1G9 (IGG1-LAMBDA) FAB FRAGMENT COMPLEXED WITH (4-HYDROXY-3-NITROPHENYL) ACETATE
Components(N1G9 (IGG1-LAMBDA)) x 2
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


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 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID / : / Anti-human Langerin 2G3 lambda chain / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsMizutani, R. / Satow, Y.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Three-dimensional structures of the Fab fragment of murine N1G9 antibody from the primary immune response and of its complex with (4-hydroxy-3-nitrophenyl)acetate.
Authors: Mizutani, R. / Miura, K. / Nakayama, T. / Shimada, I. / Arata, Y. / Satow, Y.
#1: Journal: Embo J. / Year: 1988
Title: Antibody Engineering for the Analysis of Affinity Maturation of an Anti-Hapten Response
Authors: Allen, D. / Simon, T. / Sablitzky, F. / Rajewsky, K. / Cumano, A.
#2: Journal: Eur.J.Immunol. / Year: 1985
Title: Structure of Primary Anti-(4-Hydroxy-3-Nitrophenyl)Acetyl (Np) Antibodies in Normal and Idiotypically Suppressed C57Bl/6 Mice
Authors: Cumano, A. / Rajewsky, K.
#3: Journal: Nature / Year: 1982
Title: Somatic Variants of Murine Immunoglobulin Lambda Light Chains
Authors: Bothwell, A.L. / Paskind, M. / Reth, M. / Imanishi-Kari, T. / Rajewsky, K. / Baltimore, D.
History
DepositionJun 23, 1995Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_entry_details.has_protein_modification / _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: N1G9 (IGG1-LAMBDA)
H: N1G9 (IGG1-LAMBDA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5054
Polymers47,2122
Non-polymers2932
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-34 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.691, 110.691, 98.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody N1G9 (IGG1-LAMBDA)


Mass: 23129.604 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: C57BL/6 / References: GenBank: 387376, UniProt: G0YP42*PLUS
#2: Antibody N1G9 (IGG1-LAMBDA)


Mass: 24082.002 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: C57BL/6 / References: UniProt: P01751
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NPA / 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID


Mass: 197.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7NO5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE NUMBERING SYSTEM USED IN THIS ENTRY IS SEQUENTIAL, FROM 1 TO 211 FOR THE LIGHT CHAIN AND FROM 1 ...THE NUMBERING SYSTEM USED IN THIS ENTRY IS SEQUENTIAL, FROM 1 TO 211 FOR THE LIGHT CHAIN AND FROM 1 TO 220 FOR THE HEAVY CHAIN. THE CONVERSION TO KABAT NUMBERING (E.A.KABAT,T.T.WU, M.REID-MILLER, H.M.PERRY, AND K.S.GOTTESMAN (1991) SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 5TH ED., NATIONAL INSTITUTES OF HEALTH BETHESDA, MD) FOR THE FAB REGIONS OF THE LIGHT AND HEAVY CHAINS IS GIVEN BELOW. SEQUENTIAL NUMBERING KABAT NUMBERING LIGHT CHAIN 1 - 9 1 - 9 10 - 26 11 - 27 27 27A 28 27B 29 27C 30 - 108 28 - 106 109 106A 110 - 171 107 - 168 172 - 202 170 - 200 203 - 215 203 - 215 HEAVY CHAIN 1 - 52 1 - 52 53 52A 54 - 83 53 - 82 84 82A 85 82B 86 82C 87 - 104 83 - 100 105 100A 106 100J 107 100K 108 - 137 101 - 130 138 - 159 133 - 154 160 - 161 156 - 157 162 - 169 162 - 169 170 - 179 171 - 180 180 - 193 183 - 196 194 - 195 199 - 200 196 - 217 202 - 223 218 - 221 226 - 229 222 235

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.5 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 10 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8-1.9 Mammonium salfate1reservoir
20.1 MTris1reservoir
310 mg/mlFab solution1drop
41.8-1.9 Mammonium salfate1drop
50.1 MTris1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Type: PHOTON FACTORY / Wavelength: 0.8931
DetectorType: SATOW / Detector: IMAGE PLATE / Date: Feb 22, 1994 / Details: DOUBLE CRYSTAL MONOCHROMATOR / PT MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8931 Å / Relative weight: 1
ReflectionResolution: 2.4→19 Å / Num. obs: 21761 / % possible obs: 89.3 % / Observed criterion σ(I): 0 / Redundancy: 3.51 % / Rmerge(I) obs: 0.066
Reflection
*PLUS
Lowest resolution: 15 Å / % possible obs: 89 % / Num. measured all: 76319
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.6 Å / % possible obs: 68 %

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Processing

Software
NameVersionClassification
OSCMGRdata collection
X-PLOR2.1model building
PROLSQrefinement
X-PLOR2.1refinement
OSCdata reduction
X-PLOR2.1phasing
RefinementResolution: 2.4→15 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.25 -10 %
Rwork0.196 --
obs-21708 89.3 %
Displacement parametersBiso mean: 26.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 19 134 3383
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0390.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0490.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8911
X-RAY DIFFRACTIONp_mcangle_it1.621.5
X-RAY DIFFRACTIONp_scbond_it3.4643
X-RAY DIFFRACTIONp_scangle_it5.1594
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.170.15
X-RAY DIFFRACTIONp_singtor_nbd0.130.5
X-RAY DIFFRACTIONp_multtor_nbd0.2350.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.230.5
X-RAY DIFFRACTIONp_planar_tor2.43
X-RAY DIFFRACTIONp_staggered_tor2215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.820
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.25 / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS

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