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- PDB-2bjm: SPE7:Anthrone Complex -

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Basic information

Entry
Database: PDB / ID: 2bjm
TitleSPE7:Anthrone Complex
Components
  • IGE SPE7 HEAVY CHAIN
  • IGE SPE7 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / ENCOUNTER COMPLEX
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / immune response
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ANTHRONE / Ig lambda-1 chain V regions MOPC 104E/RPC20/J558/S104
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJames, L.C. / Tawfik, D.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structure and Kinetics of a Transient Antibody Binding Intermediate Reveal a Kinetic Discrimination Mechanism in Antigen Recognition
Authors: James, L.C. / Tawfik, D.S.
History
DepositionFeb 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Derived calculations / Other ...Derived calculations / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: IGE SPE7 HEAVY CHAIN
L: IGE SPE7 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2983
Polymers25,1042
Non-polymers1941
Water00
1
H: IGE SPE7 HEAVY CHAIN
L: IGE SPE7 LIGHT CHAIN
hetero molecules

H: IGE SPE7 HEAVY CHAIN
L: IGE SPE7 LIGHT CHAIN
hetero molecules

H: IGE SPE7 HEAVY CHAIN
L: IGE SPE7 LIGHT CHAIN
hetero molecules

H: IGE SPE7 HEAVY CHAIN
L: IGE SPE7 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,19312
Polymers100,4168
Non-polymers7774
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area13490 Å2
ΔGint-71.8 kcal/mol
Surface area38930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.672, 79.672, 67.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Antibody IGE SPE7 HEAVY CHAIN


Mass: 13545.160 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, RESIDUES 1-120
Source method: isolated from a genetically manipulated source
Details: ANTHRONE ATTACHED / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli)
#2: Antibody IGE SPE7 LIGHT CHAIN


Mass: 11558.817 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN, RESIDUES 1-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01724*PLUS
#3: Chemical ChemComp-ANF / ANTHRONE


Mass: 194.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 46 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→56 Å / Num. obs: 11647 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.4
Reflection shellResolution: 2.1→2.25 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.4 / % possible all: 97

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→56.34 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.813 / SU B: 8.242 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.2 / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 287 4.77 %RANDOM
Rwork0.268 ---
obs0.269 6123 52.5 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 31.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.161 Å2
Refinement stepCycle: LAST / Resolution: 2.15→56.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 15 0 1782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221830
X-RAY DIFFRACTIONr_bond_other_d0.0040.023120
X-RAY DIFFRACTIONr_angle_refined_deg1.9471.9442492
X-RAY DIFFRACTIONr_angle_other_deg3.14537281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2925228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27923.83673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.88815281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.534157
X-RAY DIFFRACTIONr_chiral_restr0.1350.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021383
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02581
X-RAY DIFFRACTIONr_nbd_refined0.3050.2858
X-RAY DIFFRACTIONr_nbd_other0.2410.33043
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21135
X-RAY DIFFRACTIONr_nbtor_other0.4470.517
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4480.296
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.381
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2870.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8661.51176
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.59421818
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7293774
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7114.5674
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 9.48→56.34 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.787 5
Rwork0.301 74

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