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- PDB-1mlb: MONOCLONAL ANTIBODY FAB D44.1 RAISED AGAINST CHICKEN EGG-WHITE LY... -

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Basic information

Entry
Database: PDB / ID: 1mlb
TitleMONOCLONAL ANTIBODY FAB D44.1 RAISED AGAINST CHICKEN EGG-WHITE LYSOZYME
Components
  • IGG1-KAPPA D44.1 FAB (HEAVY CHAIN)
  • IGG1-KAPPA D44.1 FAB (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN
Function / homology
Function and homology information


B cell differentiation / extracellular region / plasma membrane
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
: / Immunoglobulin kappa constant
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsBraden, B.C. / Souchon, H. / Eisele, J.-L. / Bentley, G.A. / Bhat, T.N. / Navaza, J. / Poljak, R.J.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Three-dimensional structures of the free and the antigen-complexed Fab from monoclonal anti-lysozyme antibody D44.1.
Authors: Braden, B.C. / Souchon, H. / Eisele, J.L. / Bentley, G.A. / Bhat, T.N. / Navaza, J. / Poljak, R.J.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Two Antigen-Antibody (Lysozyme-Fab) Complexes
Authors: Fischmann, T. / Souchon, H. / Riottot, M.-M. / Tello, D. / Poljak, R.J.
History
DepositionMar 8, 1995Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2013Group: Source and taxonomy
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IGG1-KAPPA D44.1 FAB (LIGHT CHAIN)
B: IGG1-KAPPA D44.1 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,8262
Polymers46,8262
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-24 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.700, 136.200, 43.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 8 / 2: CIS PROLINE - PRO A 95 / 3: CIS PROLINE - PRO A 141 / 4: CIS PROLINE - PRO B 150 / 5: CIS PROLINE - PRO B 152 / 6: CIS PROLINE - PRO B 192

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Components

#1: Antibody IGG1-KAPPA D44.1 FAB (LIGHT CHAIN)


Mass: 23609.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01837
#2: Antibody IGG1-KAPPA D44.1 FAB (HEAVY CHAIN)


Mass: 23215.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: PIR: PC4202
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Compound detailsVL RESIDUE SER 30 IS IN THE SECOND POSITION OF A II'-TYPE TURN. VL RESIDUE VAL 51 IS THE SECOND ...VL RESIDUE SER 30 IS IN THE SECOND POSITION OF A II'-TYPE TURN. VL RESIDUE VAL 51 IS THE SECOND RESIDUE (I+1) OF A MODIFIED GAMMA TURN (CLASS 3).
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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlPEG1drop
212 %(w/v)PEG40001drop
30.1 Mcitrate1drop

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 26986 / % possible obs: 70 % / Redundancy: 4 % / Rmerge(I) obs: 0.1
Reflection
*PLUS
Highest resolution: 2.1 Å / Rmerge(I) obs: 0.1 / Num. measured all: 106016

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Processing

Software
NameClassification
XDSdata scaling
PROLSQrefinement
XDSdata reduction
RefinementResolution: 2.1→7 Å / σ(F): 2
Details: D44.1 IS CRYSTALLIZED AS THE FAB. CHAIN A INCLUDES THE VL AND CL DOMAINS. CHAIN B INCLUDES THE VH AND CH1 DOMAINS. CHAIN B RESIDUES 131 - 136, ASP 217 AND THE C-TERMINAL CYS 218 (ALL IN THE ...Details: D44.1 IS CRYSTALLIZED AS THE FAB. CHAIN A INCLUDES THE VL AND CL DOMAINS. CHAIN B INCLUDES THE VH AND CH1 DOMAINS. CHAIN B RESIDUES 131 - 136, ASP 217 AND THE C-TERMINAL CYS 218 (ALL IN THE CH1 DOMAIN) HAVE NO ELECTRON DENSITY AND, THEREFORE, THE ATOMIC POSITIONS FOR THESE RESIDUES SHOULD BE CONSIDERED ARBITRARY.
RfactorNum. reflection
Rfree0.274 -
obs0.181 19168
Displacement parametersBiso mean: 27.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 0 0 115 3405
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0410.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8611
X-RAY DIFFRACTIONp_mcangle_it1.531.5
X-RAY DIFFRACTIONp_scbond_it1.391.5
X-RAY DIFFRACTIONp_scangle_it2.22
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1550.15
X-RAY DIFFRACTIONp_singtor_nbd0.210.4
X-RAY DIFFRACTIONp_multtor_nbd0.250.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.230.4
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.43
X-RAY DIFFRACTIONp_staggered_tor21.115
X-RAY DIFFRACTIONp_orthonormal_tor19.820
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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