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- PDB-2a77: Anti-Cocaine Antibody 7.5.21, Crystal Form II -

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Basic information

Entry
Database: PDB / ID: 2a77
TitleAnti-Cocaine Antibody 7.5.21, Crystal Form II
Components
  • Immunoglobulin Heavy Chain
  • Immunoglobulin Light Chain
KeywordsIMMUNE SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPozharski, E. / Hewagama, A. / Shanafelt, A. / Ringe, D. / Petsko, G.A.
CitationJournal: To be Published
Title: Flexibility of Packing: Four Crystal Forms of an Anti-Cocaine Antibody 7.5.21
Authors: Pozharski, E. / Hewagama, A. / Shanafelt, A. / Ringe, D. / Petsko, G.A.
History
DepositionJul 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 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: Immunoglobulin Light Chain
H: Immunoglobulin Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,98315
Polymers47,7622
Non-polymers1,22113
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-105 kcal/mol
Surface area19700 Å2
MethodPISA
2
L: Immunoglobulin Light Chain
H: Immunoglobulin Heavy Chain
hetero molecules

L: Immunoglobulin Light Chain
H: Immunoglobulin Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,96730
Polymers95,5254
Non-polymers2,44226
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area13880 Å2
ΔGint-235 kcal/mol
Surface area38040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.410, 81.857, 61.608
Angle α, β, γ (deg.)90.00, 112.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Immunoglobulin Light Chain


Mass: 23893.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: hybridoma / Strain: BALB/C
#2: Antibody Immunoglobulin Heavy Chain


Mass: 23868.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: hybridoma / Strain: BALB/C
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16% PEG8000, 0.3M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.89996 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89996 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 46600 / Num. obs: 46600 / % possible obs: 97 % / Observed criterion σ(F): 0 / Redundancy: 4 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.044 / Χ2: 1.124 / Net I/σ(I): 33
Reflection shellResolution: 1.8→1.86 Å / % possible obs: 87.2 % / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.7 / Num. measured obs: 4182 / Num. unique all: 4182 / Χ2: 0.971 / % possible all: 87.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A1W

2a1w


Resolution: 1.8→33.3 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.041 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2356 5.1 %RANDOM
Rwork0.218 ---
all0.22 46597 --
obs-46597 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.947 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20.02 Å2
2--1.94 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 72 318 3718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223522
X-RAY DIFFRACTIONr_angle_refined_deg2.041.9664797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3535445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94523.504137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.12615551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8531518
X-RAY DIFFRACTIONr_chiral_restr0.1440.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022627
X-RAY DIFFRACTIONr_nbd_refined0.230.21593
X-RAY DIFFRACTIONr_nbtor_refined0.310.22283
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2307
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.214
X-RAY DIFFRACTIONr_mcbond_it1.2681.52246
X-RAY DIFFRACTIONr_mcangle_it1.90623555
X-RAY DIFFRACTIONr_scbond_it2.81531479
X-RAY DIFFRACTIONr_scangle_it3.914.51236
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 168 -
Rwork0.317 2842 -
all-3010 -
obs--84.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5950.22950.0570.9256-1.00713.44060.0731-0.32120.1734-0.0309-0.03460.11-0.0292-0.0352-0.0386-0.16260.01580.0177-0.0860.025-0.05425.97353.333423.4679
21.6988-0.29950.06540.6967-1.02492.49630.03520.15850.0444-0.0509-0.0866-0.0602-0.15970.09190.0514-0.09480.04070.0079-0.10180.0442-0.140738.5123-4.686111.3162
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LA1 - 1121 - 112
21HB1 - 1231 - 122
32LA113 - 216113 - 216
42HB124 - 223123 - 222

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