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- PDB-2g2r: Green-fluorescent antibody 11G10 in complex with its hapten (nitr... -

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Basic information

Entry
Database: PDB / ID: 2g2r
TitleGreen-fluorescent antibody 11G10 in complex with its hapten (nitro-stilbene derivative)
Components
  • Green-fluorescent antibody (11G10)-heavy chain
  • Green-fluorescent antibody (11G10)-light chain
KeywordsIMMUNE SYSTEM / immunoglobulin / green-fluorescent antibody / stilbene-complex
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / extracellular region
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
Chem-TNS / Ig heavy chain Mem5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.75 Å
AuthorsDebler, E.W. / Wilson, I.A.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2006
Title: The Effects of Antibodies on Stilbene Excited-State Energetics.
Authors: Tian, F. / Debler, E.W. / Millar, D.P. / Deniz, A.A. / Wilson, I.A. / Schultz, P.G.
History
DepositionFeb 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE According to authors, the aminoacid sequence for the proteins in this entry has not yet ...SEQUENCE According to authors, the aminoacid sequence for the proteins in this entry has not yet been deposited in any protein sequence database

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Green-fluorescent antibody (11G10)-light chain
H: Green-fluorescent antibody (11G10)-heavy chain
A: Green-fluorescent antibody (11G10)-light chain
B: Green-fluorescent antibody (11G10)-heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7659
Polymers95,7684
Non-polymers9975
Water2,162120
1
L: Green-fluorescent antibody (11G10)-light chain
H: Green-fluorescent antibody (11G10)-heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3344
Polymers47,8842
Non-polymers4502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-49 kcal/mol
Surface area20470 Å2
MethodPISA
2
A: Green-fluorescent antibody (11G10)-light chain
B: Green-fluorescent antibody (11G10)-heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4305
Polymers47,8842
Non-polymers5473
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-36 kcal/mol
Surface area20610 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11550 Å2
ΔGint-98 kcal/mol
Surface area38790 Å2
MethodPISA
4
L: Green-fluorescent antibody (11G10)-light chain
H: Green-fluorescent antibody (11G10)-heavy chain
hetero molecules

A: Green-fluorescent antibody (11G10)-light chain
B: Green-fluorescent antibody (11G10)-heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7659
Polymers95,7684
Non-polymers9975
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1/2,y+1/2,-z1
Buried area10660 Å2
ΔGint-98 kcal/mol
Surface area39690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.788, 53.761, 110.390
Angle α, β, γ (deg.)90.00, 94.64, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21A
12L
22A
13H
23B
14H
24B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLYSLYSLA1 - 1071 - 112
21ASPASPLYSLYSAC1 - 1071 - 112
12ARGARGCYSCYSLA108 - 214113 - 219
22ARGARGCYSCYSAC108 - 214113 - 219
13GLNGLNTHRTHRHB1 - 1131 - 118
23GLNGLNTHRTHRBD1 - 1131 - 118
14ALAALAGLYGLYHB114 - 229119 - 219
24ALAALAGLYGLYBD114 - 229119 - 219

NCS ensembles :
ID
1
2
3
4
DetailsThis entry contains the crystallographic asymmetric unit which consists of 2 biological molecules: LH and AB

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Components

#1: Antibody Green-fluorescent antibody (11G10)-light chain


Mass: 24202.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Purified from ascitic fluid / Source: (natural) Mus musculus (house mouse) / Strain: Swiss Webster
#2: Antibody Green-fluorescent antibody (11G10)-heavy chain


Mass: 23681.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Purified from ascitic fluid / Source: (natural) Mus musculus (house mouse) / Strain: Swiss Webster / References: UniProt: P84751
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TNS / N-(TRANS-4'-NITRO-4-STILBENYL)-N-METHYL-5-AMINO-PENTANOIC ACID / 5-[{4-[(E)-2-(4-NITROPHENYL)VINYL]PHENYL}(METHYL)AMINO]PENTANOIC ACID


Mass: 354.400 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 4000, ammoniumsulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 5, 2004
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 25702 / Num. obs: 25496 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 53 Å2 / Rsym value: 0.14 / Net I/σ(I): 9.1
Reflection shellResolution: 2.75→2.81 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1677 / Rsym value: 0.552 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MIR
Starting model: PDB entry 1MRF

1mrf


Resolution: 2.75→50 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.88 / SU B: 29.968 / SU ML: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25024 1257 5 %RANDOM
Rwork0.20291 ---
all0.2053 24106 --
obs0.2053 24014 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.671 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20.36 Å2
2--0.65 Å20 Å2
3----0.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6730 0 67 120 6917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226968
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.9649500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1745872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75824.122262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.364151118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3421526
X-RAY DIFFRACTIONr_chiral_restr0.0810.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025206
X-RAY DIFFRACTIONr_nbd_refined0.210.22803
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24682
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2280
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2820.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.27
X-RAY DIFFRACTIONr_mcbond_it0.3891.54445
X-RAY DIFFRACTIONr_mcangle_it0.65427106
X-RAY DIFFRACTIONr_scbond_it1.08633059
X-RAY DIFFRACTIONr_scangle_it1.9244.52394
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1L860tight positional0.040.05
2L840tight positional0.040.05
3H934tight positional0.040.05
4H731tight positional0.040.05
1L860tight thermal0.080.5
2L840tight thermal0.080.5
3H934tight thermal0.080.5
4H731tight thermal0.10.5
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 91 -
Rwork0.327 1745 -
obs-1745 100 %

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