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- PDB-1nj9: Cocaine hydrolytic antibody 15A10 -

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Basic information

Entry
Database: PDB / ID: 1nj9
TitleCocaine hydrolytic antibody 15A10
Components
  • immunoglobulin heavy chain
  • immunoglobulin variable chain
KeywordsIMMUNE SYSTEM / immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLarsen, N.A. / de Prada, P. / Deng, S.X. / Zhu, X. / Landry, D.W. / Wilson, I.A.
Citation
Journal: Biochemistry / Year: 2004
Title: Crystallographic and biochemical analysis of cocaine-degrading antibody 15A10.
Authors: Larsen, N.A. / de Prada, P. / Deng, S.X. / Mittal, A. / Braskett, M. / Zhu, X. / Wilson, I.A. / Landry, D.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure determination of a cocaine hydrolytic antibody from a pseudomerohedrally twinned crystal.
Authors: Larsen, N.A. / Heine, A. / de Prada, P. / Redwan, E.R. / Yeates, T.O. / Landry, D.W. / Wilson, I.A.
History
DepositionDec 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Aug 14, 2019Group: Data collection / Category: computing
Revision 1.6Oct 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999Sequence an appropriate sequence database reference was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: immunoglobulin variable chain
H: immunoglobulin heavy chain
A: immunoglobulin variable chain
B: immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,17612
Polymers91,9924
Non-polymers1848
Water1,928107
1
L: immunoglobulin variable chain
H: immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1117
Polymers45,9962
Non-polymers1155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-66 kcal/mol
Surface area19540 Å2
MethodPISA
2
A: immunoglobulin variable chain
B: immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0655
Polymers45,9962
Non-polymers693
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-58 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.5, 108.4, 111.3
Angle α, β, γ (deg.)90, 90, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody immunoglobulin variable chain


Mass: 22980.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody immunoglobulin heavy chain


Mass: 23015.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 12% PEG 4000, 12-14% isopropanol, 100mM MES, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 296 K / pH: 5.5 / Method: vapor diffusion, sitting drop
Details: Larsen, N.A., (2002) Acta Crystallogr.,Sect.D, 58, 2055.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
20.2 Msodium acetate1droppH5.5
312 %PEG40001reservoir
412-14 %2-propanol1reservoir
5100 mMMES1reservoirpH5.4

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 32009 / % possible obs: 85.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 14.4
Reflection shellResolution: 2.35→2.45 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.399 / % possible all: 76.6
Reflection
*PLUS
Num. measured all: 91574
Reflection shell
*PLUS
% possible obs: 76.6 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
EPMRphasing
SHELXL-97& CNS1.1refinement
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1526 -thin shells
Rwork0.199 ---
all0.204 32009 --
obs0.201 29505 80 %-
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.29 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6464 0 8 107 6579
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0096
X-RAY DIFFRACTIONc_angle_deg1.966
X-RAY DIFFRACTIONc_dihedral_angle_d30.2
X-RAY DIFFRACTIONc_improper_angle_d1.4
Software
*PLUS
Name: SHELX / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.008
X-RAY DIFFRACTIONangle_deg1.5
X-RAY DIFFRACTIONdihedral_angle_d
X-RAY DIFFRACTIONdihedral_angle_deg27.7
X-RAY DIFFRACTIONimproper_angle_d
X-RAY DIFFRACTIONimproper_angle_deg0.99

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