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- PDB-1bln: ANTI-P-GLYCOPROTEIN FAB MRK-16 -

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Basic information

Entry
Database: PDB / ID: 1bln
TitleANTI-P-GLYCOPROTEIN FAB MRK-16
Components
  • PROTEIN (MONOCLONAL ANTIBODY MRK-16 (HEAVY CHAIN))
  • PROTEIN (MONOCLONAL ANTIBODY MRK-16 (LIGHT CHAIN))
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVasudevan, S. / Tsuruo, T. / Rose, D.R.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: Mode of binding of anti-P-glycoprotein antibody MRK-16 to its antigen. A crystallographic and molecular modeling study.
Authors: Vasudevan, S. / Tsuruo, T. / Rose, D.R.
#1: Journal: Protein Pept.Lett. / Year: 1996
Title: Preliminary Crystallographic Analysis of Anti-P-Gl Fab MRK-16 in Complex with its Antigenic Peptide
Authors: Vasudevan, S. / Johns, K. / Rose, D.R.
History
DepositionJul 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value
Revision 1.4Aug 9, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (MONOCLONAL ANTIBODY MRK-16 (LIGHT CHAIN))
B: PROTEIN (MONOCLONAL ANTIBODY MRK-16 (HEAVY CHAIN))
C: PROTEIN (MONOCLONAL ANTIBODY MRK-16 (LIGHT CHAIN))
D: PROTEIN (MONOCLONAL ANTIBODY MRK-16 (HEAVY CHAIN))


Theoretical massNumber of molelcules
Total (without water)93,9974
Polymers93,9974
Non-polymers00
Water00
1
A: PROTEIN (MONOCLONAL ANTIBODY MRK-16 (LIGHT CHAIN))
B: PROTEIN (MONOCLONAL ANTIBODY MRK-16 (HEAVY CHAIN))


Theoretical massNumber of molelcules
Total (without water)46,9982
Polymers46,9982
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-26 kcal/mol
Surface area18700 Å2
MethodPISA
2
C: PROTEIN (MONOCLONAL ANTIBODY MRK-16 (LIGHT CHAIN))
D: PROTEIN (MONOCLONAL ANTIBODY MRK-16 (HEAVY CHAIN))


Theoretical massNumber of molelcules
Total (without water)46,9982
Polymers46,9982
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-27 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.490, 67.774, 117.186
Angle α, β, γ (deg.)90.00, 97.61, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9883, 0.1522, 0.0131), (-0.1497, 0.9821, -0.1143), (-0.0303, 0.111, 0.9934)
Vector: 4.4738, -26.436, -61.4979)

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Components

#1: Antibody PROTEIN (MONOCLONAL ANTIBODY MRK-16 (LIGHT CHAIN))


Mass: 23583.145 Da / Num. of mol.: 2 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody PROTEIN (MONOCLONAL ANTIBODY MRK-16 (HEAVY CHAIN))


Mass: 23415.236 Da / Num. of mol.: 2 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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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: 2.14 Å3/Da / Density % sol: 53 %
Crystal growpH: 4 / Details: pH 4.0
Crystal grow
*PLUS
Method: other / Details: Vasudevan, S., (1994) J. Mol. Biol., 241, 736.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR
RadiationMonochromator: QUARTZ / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 18167 / % possible obs: 86 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rsym value: 0.114 / Net I/σ(I): 9.7
Reflection shellResolution: 2.8→3 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.22 / % possible all: 75
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 86 % / Num. measured all: 56513 / Rmerge(I) obs: 0.114
Reflection shell
*PLUS
% possible obs: 75 % / Num. unique obs: 3111 / Num. measured obs: 5374 / Rmerge(I) obs: 0.22

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.8refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MCP

1mcp


Resolution: 2.8→8 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.287 915 5 %RANDOM
Rwork0.209 ---
obs0.209 18736 80 %-
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6606 0 0 0 6606
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2

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