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- PDB-1mam: CRYSTAL STRUCTURE TO 2.45 A RESOLUTION OF A MONOCLONAL FAB SPECIF... -

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Basic information

Entry
Database: PDB / ID: 1mam
TitleCRYSTAL STRUCTURE TO 2.45 A RESOLUTION OF A MONOCLONAL FAB SPECIFIC FOR THE BRUCELLA A CELL WALL POLYSACCHARIDE ANTIGEN
Components
  • IGG2B-KAPPA YST9.1 FAB (HEAVY CHAIN)
  • IGG2B-KAPPA YST9.1 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / positive regulation of phagocytosis / positive regulation of immune response / extracellular space / 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 heavy constant gamma 2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.45 Å
AuthorsRose, D.R.
CitationJournal: Protein Sci. / Year: 1993
Title: Crystal structure to 2.45 A resolution of a monoclonal Fab specific for the Brucella A cell wall polysaccharide antigen.
Authors: Rose, D.R. / Przybylska, M. / To, R.J. / Kayden, C.S. / Oomen, R.P. / Vorberg, E. / Young, N.M. / Bundle, D.R.
History
DepositionJan 14, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG2B-KAPPA YST9.1 FAB (LIGHT CHAIN)
H: IGG2B-KAPPA YST9.1 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,9292
Polymers46,9292
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-30 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.730, 126.820, 46.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: THR L 43 - VAL L 44 OMEGA ANGLE = 34.342 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO L 95 / 3: CIS PROLINE - PRO L 141
4: SER H 79 - ILE H 80 OMEGA ANGLE = 139.405 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: CIS PROLINE - PRO H 105
6: GLY H 135 - ASP H 136 OMEGA ANGLE = 245.392 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: SER H 141 - VAL H 142 OMEGA ANGLE = 140.185 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
8: CIS PROLINE - PRO H 153
9: SER H 155 - VAL H 156 OMEGA ANGLE = 122.634 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
10: SER H 166 - SER H 167 OMEGA ANGLE = 263.733 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
11: CIS PROLINE - PRO H 195

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Components

#1: Antibody IGG2B-KAPPA YST9.1 FAB (LIGHT CHAIN)


Mass: 23772.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#2: Antibody IGG2B-KAPPA YST9.1 FAB (HEAVY CHAIN)


Mass: 23156.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01867
Has protein modificationY
Sequence detailsTHE RESIDUE NUMBERING IS SEQUENTIAL WITHIN EACH CHAIN. THE SEQUENTIAL NUMBERING OF THE LIGHT CHAIN ...THE RESIDUE NUMBERING IS SEQUENTIAL WITHIN EACH CHAIN. THE SEQUENTIAL NUMBERING OF THE LIGHT CHAIN CORRESPONDS TO THE KABAT NUMBERING SCHEME. THE FOLLOWING IS THE RELATIONSHIP OF THE SEQUENTIAL NUMBERING SCHEME OF THE HEAVY CHAIN TO THE KABAT NUMBERING SCHEME: 1 - 52 1 - 52 53 - 55 52A- 52C 56 - 85 53 - 82 86 - 88 82A- 82C 89 - 217 83 - END

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
20.12 Mammonium sulfate1drop0.001 ml
30.5 MTris-HCl1drop0.0008 ml
420 %(w/v)PEG80001drop0.0042 ml
534 %PEG80001reservoir0.001 ml
1Fab1drop0.004 ml
6sodium azide1reservoirtrace amount

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.42 Å / Num. all: 17763 / Num. obs: 15355 / Num. measured all: 37288 / Rmerge(I) obs: 0.0517

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.215 / Highest resolution: 2.45 Å
Refinement stepCycle: LAST / Highest resolution: 2.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 0 0 3296
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.45 Å / Num. reflection obs: 3296 / Rfactor obs: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.030.034
X-RAY DIFFRACTIONp_dihedral_angle_d32.2
X-RAY DIFFRACTIONp_plane_restr0.020.012
LS refinement shell
*PLUS
Highest resolution: 2.45 Å / Lowest resolution: 2.6 Å / Num. reflection obs: 1750 / Rfactor obs: 0.27

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