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- PDB-2pcp: ANTIBODY FAB COMPLEXED WITH PHENCYCLIDINE -

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Basic information

Entry
Database: PDB / ID: 2pcp
TitleANTIBODY FAB COMPLEXED WITH PHENCYCLIDINE
Components(IMMUNOGLOBULIN) x 2
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 1-(PHENYL-1-CYCLOHEXYL)PIPERIDINE / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLim, K. / Owens, S.M. / Arnold, L. / Sacchettini, J.C. / Linthicum, D.S.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Crystal structure of monoclonal 6B5 Fab complexed with phencyclidine.
Authors: Lim, K. / Owens, S.M. / Arnold, L. / Sacchettini, J.C. / Linthicum, D.S.
History
DepositionJun 2, 1998Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IMMUNOGLOBULIN
B: IMMUNOGLOBULIN
C: IMMUNOGLOBULIN
D: IMMUNOGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6836
Polymers94,1974
Non-polymers4872
Water12,214678
1
A: IMMUNOGLOBULIN
B: IMMUNOGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3423
Polymers47,0982
Non-polymers2431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-31 kcal/mol
Surface area19170 Å2
MethodPISA
2
C: IMMUNOGLOBULIN
D: IMMUNOGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3423
Polymers47,0982
Non-polymers2431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-31 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.460, 67.720, 68.040
Angle α, β, γ (deg.)62.11, 84.66, 83.17
Int Tables number1
Space group name H-MP1
DetailsTHERE ARE TWO FAB MOLECULES IN THE ASYMMETRIC UNIT. THE LIGHT CHAINS ARE NAMED A AND C, AND THE HEAVY CHAINS ARE NAMED B AND D.

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Components

#1: Antibody IMMUNOGLOBULIN


Mass: 23850.471 Da / Num. of mol.: 2 / Fragment: FAB / Source method: isolated from a natural source
Details: COMPLEXED WITH 1-(1-PHENYLCYCLOHEXYL) PIPERIDINE (PCP, OR PHENCYCLIDINE)
Source: (natural) Mus musculus (house mouse) / References: PIR: PC4203
#2: Antibody IMMUNOGLOBULIN


Mass: 23247.877 Da / Num. of mol.: 2 / Fragment: FAB / Source method: isolated from a natural source
Details: COMPLEXED WITH 1-(1-PHENYLCYCLOHEXYL) PIPERIDINE (PCP, OR PHENCYCLIDINE)
Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-1PC / 1-(PHENYL-1-CYCLOHEXYL)PIPERIDINE / PHENCYCLIDINE


Mass: 243.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H25N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FAB MOLECULES ARE NUMBERED ACCORDING TO KABAT (E.A.KABAT, T.T.WU, H.M.PERRY, K.S.GOTTESMAN, AND ...THE FAB MOLECULES ARE NUMBERED ACCORDING TO KABAT (E.A.KABAT, T.T.WU, H.M.PERRY, K.S.GOTTESMAN, AND C.FOELLER, SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 1991).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
22.2 Mammonium sulfate1reservoir
30.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 33694 / % possible obs: 79.3 % / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 9.8
Reflection shellResolution: 2.2→2.4 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.221 / % possible all: 63.5
Reflection
*PLUS
Num. measured all: 69236
Reflection shell
*PLUS
% possible obs: 63.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FAB AND 1GIG

4fab

1gig


Resolution: 2.2→6 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.29 3074 7.8 %RANDOM
Rwork0.196 ---
obs0.196 31830 78.7 %-
Displacement parametersBiso mean: 23.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6628 0 36 678 7342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.1
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.199 / Rfactor Rfree: 0.286
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.3

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