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- PDB-2a1w: Anti-cocaine antibody 7.5.21, crystal form I -

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Basic information

Entry
Database: PDB / ID: 2a1w
TitleAnti-cocaine antibody 7.5.21, crystal form I
Components
  • immunoglobulin heavy chain
  • immunoglobulin light chain kappa
KeywordsIMMUNE SYSTEM
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 C1-set domain ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
If kappa light chain / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionJun 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: immunoglobulin light chain kappa
H: immunoglobulin heavy chain
M: immunoglobulin light chain kappa
I: immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,01611
Polymers96,3444
Non-polymers6727
Water2,234124
1
L: immunoglobulin light chain kappa
H: immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3644
Polymers48,1722
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-57 kcal/mol
Surface area20820 Å2
MethodPISA
2
M: immunoglobulin light chain kappa
I: immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6527
Polymers48,1722
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-66 kcal/mol
Surface area20230 Å2
MethodPISA
3
L: immunoglobulin light chain kappa
H: immunoglobulin heavy chain
M: immunoglobulin light chain kappa
I: immunoglobulin heavy chain
hetero molecules

L: immunoglobulin light chain kappa
H: immunoglobulin heavy chain
M: immunoglobulin light chain kappa
I: immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,03222
Polymers192,6878
Non-polymers1,34514
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area20910 Å2
ΔGint-328 kcal/mol
Surface area78690 Å2
MethodPISA
4
M: immunoglobulin light chain kappa
I: immunoglobulin heavy chain
hetero molecules

M: immunoglobulin light chain kappa
I: immunoglobulin heavy chain
hetero molecules

L: immunoglobulin light chain kappa
H: immunoglobulin heavy chain
hetero molecules

L: immunoglobulin light chain kappa
H: immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,03222
Polymers192,6878
Non-polymers1,34514
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_656-x+3/2,y+1/2,-z+11
Buried area21710 Å2
ΔGint-317 kcal/mol
Surface area77890 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-137 kcal/mol
Surface area39720 Å2
MethodPISA
6
M: immunoglobulin light chain kappa
I: immunoglobulin heavy chain
hetero molecules

L: immunoglobulin light chain kappa
H: immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,01611
Polymers96,3444
Non-polymers6727
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_656-x+3/2,y+1/2,-z+11
Buried area10300 Å2
ΔGint-131 kcal/mol
Surface area39320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.601, 58.395, 98.098
Angle α, β, γ (deg.)90.00, 110.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody immunoglobulin light chain kappa


Mass: 23921.623 Da / Num. of mol.: 2 / Fragment: Fab fragment, light chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: hybridoma / Strain: BALB/C / References: UniProt: A2NHM3*PLUS
#2: Antibody immunoglobulin heavy chain /


Mass: 24250.188 Da / Num. of mol.: 2 / Fragment: Fab fragment, heavy chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: hybridoma / Strain: BALB/C / References: UniProt: Q99LC4*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 16% PEG8000, 0.3M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationMonochromator: Supper Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30.5 Å / Num. all: 26324 / Num. obs: 26324 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 52.6 Å2 / Rmerge(I) obs: 0.174 / Χ2: 1.088 / Net I/σ(I): 10.6
Reflection shellResolution: 2.7→2.8 Å / % possible obs: 100 % / Redundancy: 4.8 % / Mean I/σ(I) obs: 2 / Num. measured obs: 2612 / Num. unique all: 2612 / Χ2: 1.015 / % possible all: 99.96

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.601data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30.5 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.901 / SU B: 27.089 / SU ML: 0.271 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1334 5.1 %RANDOM
Rwork0.185 ---
all0.188 24967 --
obs0.188 24967 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.378 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å2-0.61 Å2
2---0.69 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6776 0 35 124 6935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226984
X-RAY DIFFRACTIONr_angle_refined_deg1.1841.9579514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0675878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58123.406276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.979151102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4971538
X-RAY DIFFRACTIONr_chiral_restr0.0790.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025276
X-RAY DIFFRACTIONr_nbd_refined0.2010.22607
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24615
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2266
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.216
X-RAY DIFFRACTIONr_mcbond_it0.4481.54500
X-RAY DIFFRACTIONr_mcangle_it0.80527132
X-RAY DIFFRACTIONr_scbond_it0.89532875
X-RAY DIFFRACTIONr_scangle_it1.5114.52382
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 --
Rwork0.263 1843 -
obs--98.22 %
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)
10.9705-0.39070.07823.53790.82961.6476-0.00660.08120.0337-0.01020.0012-0.103-0.00920.18020.0054-0.17960.06920.03840.1071-0.0064-0.1661113.100548.095767.8818
22.05050.59690.57692.36771.12455.5970.0559-0.016-0.2218-0.1130.0503-0.15470.1957-0.1973-0.1062-0.1636-0.03450.0318-0.1561-0.0326-0.0825117.527128.861898.3403
31.15060.31450.3542.5003-0.45721.6035-0.09370.00510.08020.1582-0.0259-0.1354-0.24190.25720.1196-0.0718-0.0641-0.0087-0.04960.0172-0.076394.988367.911844.1583
42.20821.93711.30125.66121.90332.2969-0.30830.17970.2725-0.52890.15410.3213-0.65440.0090.15410.0844-0.086-0.028-0.22420.0139-0.068174.534788.484724.2754
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 - 123
32LA113 - 216113 - 216
42HB124 - 225124 - 225
53MC1 - 1121 - 112
63ID1 - 1231 - 123
74MC113 - 216113 - 216
84ID124 - 225124 - 225

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