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- PDB-1bfo: CAMPATH-1G IGG2B RAT MONOCLONAL FAB -

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Basic information

Entry
Database: PDB / ID: 1bfo
TitleCAMPATH-1G IGG2B RAT MONOCLONAL FAB
Components(CAMPATH-1G ANTIBODY) x 2
KeywordsANTIBODY / FAB / CAMPATH-1G / CD52
Function / homology
Function and homology information


immunoglobulin receptor binding / immunoglobulin complex, circulating / complement activation, classical pathway / antigen binding / antibacterial humoral response
Similarity search - Function
: / 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 / Immunoglobulin-like fold ...: / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / : / Ig kappa chain C region, B allele / Ig gamma-2B chain C region
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCheetham, G.M.T. / Hale, G. / Waldmann, H. / Bloomer, A.C.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Crystal structures of a rat anti-CD52 (CAMPATH-1) therapeutic antibody Fab fragment and its humanized counterpart.
Authors: Cheetham, G.M. / Hale, G. / Waldmann, H. / Bloomer, A.C.
History
DepositionMay 20, 1998Processing site: BNL
Revision 1.0Mar 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAMPATH-1G ANTIBODY
B: CAMPATH-1G ANTIBODY
C: CAMPATH-1G ANTIBODY
D: CAMPATH-1G ANTIBODY
E: CAMPATH-1G ANTIBODY
F: CAMPATH-1G ANTIBODY
G: CAMPATH-1G ANTIBODY
H: CAMPATH-1G ANTIBODY


Theoretical massNumber of molelcules
Total (without water)187,1508
Polymers187,1508
Non-polymers00
Water6,972387
1
A: CAMPATH-1G ANTIBODY
B: CAMPATH-1G ANTIBODY


Theoretical massNumber of molelcules
Total (without water)46,7872
Polymers46,7872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-24 kcal/mol
Surface area18970 Å2
MethodPISA
2
C: CAMPATH-1G ANTIBODY
D: CAMPATH-1G ANTIBODY


Theoretical massNumber of molelcules
Total (without water)46,7872
Polymers46,7872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-24 kcal/mol
Surface area18730 Å2
MethodPISA
3
E: CAMPATH-1G ANTIBODY
F: CAMPATH-1G ANTIBODY


Theoretical massNumber of molelcules
Total (without water)46,7872
Polymers46,7872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-24 kcal/mol
Surface area18780 Å2
MethodPISA
4
G: CAMPATH-1G ANTIBODY
H: CAMPATH-1G ANTIBODY


Theoretical massNumber of molelcules
Total (without water)46,7872
Polymers46,7872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-25 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.280, 108.150, 166.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99985, -0.0148, 0.00952), (0.01612, 0.98725, -0.15835), (-0.00706, 0.15848, 0.98734)-0.8958, 22.6902, -43.60738
2given(0.99988, -0.01321, 0.00771), (0.01419, 0.98938, -0.14465), (-0.00571, 0.14474, 0.98945)0.2631, 1.48896, 79.34945
3given(1, 0.0015, -0.00027), (-0.0015, 0.99993, 0.01152), (0.00029, -0.01152, 0.99993)-0.01072, -2.09713, 41.24548
4given(0.99969, -0.01353, 0.02083), (0.01654, 0.98828, -0.15174), (-0.01853, 0.15204, 0.9882)-2.64081, 21.81482, -43.37776
5given(0.99968, -0.01166, 0.02246), (0.0146, 0.99069, -0.13537), (-0.02067, 0.13566, 0.99054)-0.13803, 1.34039, 79.8312
6given(1, -0.00097, 0.00021), (0.00097, 0.99985, 0.01709), (-0.00023, -0.01709, 0.99985)-0.01343, -2.59728, 41.33634
7given(0.99982, -0.01396, 0.01253), (0.01384, 0.99986, 0.00938), (-0.01266, -0.0092, 0.99988)-0.99241, -0.15637, -40.67351
8given(0.99977, -0.01213, 0.01783), (0.01267, 0.99946, -0.03032), (-0.01745, 0.03054, 0.99938)0.47702, 0.11285, 82.49768
9given(0.99991, 0.00391, 0.01284), (-0.00304, 0.99771, -0.06761), (-0.01307, 0.06757, 0.99763)-0.72399, 2.20334, 38.85812
10given(0.99984, -0.01699, 0.00616), (0.01694, 0.99982, 0.00857), (-0.0063, -0.00846, 0.99994)-0.0156, -0.16374, -40.92933
11given(0.99989, -0.013, 0.00698), (0.01312, 0.99977, -0.01699), (-0.00675, 0.01708, 0.99983)0.58564, 0.11642, 82.76543
12given(1, 0.00232, 0.00104), (-0.00228, 0.99949, -0.03176), (-0.00111, 0.03176, 0.99949)-0.14544, 0.49609, 40.02153

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Components

#1: Antibody
CAMPATH-1G ANTIBODY


Mass: 23524.322 Da / Num. of mol.: 4 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Rattus rattus (black rat) / Secretion: ASCITIC FLUID / References: GenBank: 4096754, UniProt: P01835*PLUS
#2: Antibody
CAMPATH-1G ANTIBODY


Mass: 23263.066 Da / Num. of mol.: 4 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Rattus rattus (black rat) / Secretion: ASCITIC FLUID / References: GenBank: 1220486, UniProt: P20761*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.3 Å3/Da / Density % sol: 36 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
220 %PEG100001reservoir
30.2 Mimidazole/malate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1994 / Details: MIRRORS
RadiationMonochromator: MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 47690 / % possible obs: 90.5 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 53.3 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.33 / % possible all: 78.6
Reflection
*PLUS
Redundancy: 2.1 %
Reflection shell
*PLUS
% possible obs: 78.6 % / Rmerge(I) obs: 0.327

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATA/AGROVATAdata reduction
CNS0.3refinement
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CNS0.3phasing
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTIALLY REFINED CAMPATH-1H

Resolution: 2.6→20 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
Details: EACH OF FAB DOMAINS VL, CL, VH AND CH1 COORDINATES AND TEMPERATURE FACTORS RESTRAINED TO BE EQUAL IN EACH OF FOUR MOLECULES WITH CNS NCS POSITIONAL RESTRAINTS = 300.00 KCAL/MOL-A**2 AND B ...Details: EACH OF FAB DOMAINS VL, CL, VH AND CH1 COORDINATES AND TEMPERATURE FACTORS RESTRAINED TO BE EQUAL IN EACH OF FOUR MOLECULES WITH CNS NCS POSITIONAL RESTRAINTS = 300.00 KCAL/MOL-A**2 AND B FACTOR TARGET DEVIATION = 0.5A**2. NO NCS RESTRAINTS APPLIED TO RESIDUES IN ELBOW REGION OF EACH FAB.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1919 3.6 %RANDOM
Rwork0.192 ---
obs0.192 47690 90.5 %-
Solvent computationSolvent model: COMBINATION / Bsol: 50 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 46.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.674 Å20 Å20 Å2
2--0.657 Å20 Å2
3----5.331 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13136 0 0 388 13524
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.18
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.356 109 2.1 %
Rwork0.296 2175 -
obs--43.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1
LS refinement shell
*PLUS
Rfactor obs: 0.296

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