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- PDB-2ap2: SINGLE CHAIN FV OF C219 IN COMPLEX WITH SYNTHETIC EPITOPE PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 2ap2
TitleSINGLE CHAIN FV OF C219 IN COMPLEX WITH SYNTHETIC EPITOPE PEPTIDE
Components
  • P-GLYCOPROTEIN
  • SINGLE CHAIN FV
KeywordsIMMUNE SYSTEM / SINGLE CHAIN FV / MONOCLONAL ANTIBODY / C219 / P-GLYCOPROTEIN / IMMUNOGLOBULIN
Function / homology
Function and homology information


terpenoid transport / ceramide floppase activity / floppase activity / ABC-type oligopeptide transporter activity / phosphatidylethanolamine flippase activity / xenobiotic transport across blood-brain barrier / phosphatidylcholine floppase activity / xenobiotic detoxification by transmembrane export across the plasma membrane / intercellular canaliculus / ABC-type xenobiotic transporter ...terpenoid transport / ceramide floppase activity / floppase activity / ABC-type oligopeptide transporter activity / phosphatidylethanolamine flippase activity / xenobiotic transport across blood-brain barrier / phosphatidylcholine floppase activity / xenobiotic detoxification by transmembrane export across the plasma membrane / intercellular canaliculus / ABC-type xenobiotic transporter / P-type phospholipid transporter / ABC-type xenobiotic transporter activity / IgG immunoglobulin complex / phospholipid translocation / efflux transmembrane transporter activity / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / apical plasma membrane / ATP hydrolysis activity / extracellular exosome / ATP binding / cytoplasm
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / Immunoglobulin V-Type / ABC transporter / ABC transporter-like, ATP-binding domain ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / Immunoglobulin V-Type / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
ATP-dependent translocase ABCB1 / Igh protein / ScFv B8E5 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Cricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVan Den Elsen, J.M.H. / Rose, D.R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Antibody C219 recognizes an alpha-helical epitope on P-glycoprotein.
Authors: van Den Elsen, J.M. / Kuntz, D.A. / Hoedemaeker, F.J. / Rose, D.R.
#1: Journal: J.Biol.Chem. / Year: 1997
Title: A single chain Fv fragment of P-glycoprotein-specific monoclonal antibody C219. Design, expression, and crystal structure at 2.4 A resolution.
Authors: Hoedemaeker, F.J. / Signorelli, T. / Johns, K. / Kuntz, D.A. / Rose, D.R.
History
DepositionMar 22, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 7, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / diffrn_source ...atom_site / diffrn_source / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal_grow / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_entry_details / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _diffrn_source.source / _entity_src_gen.entity_id / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _entity_src_gen.pdbx_src_id / _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details / _pdbx_entity_nonpoly.entity_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Nov 13, 2019Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Aug 23, 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

Downloads & links

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Assembly

Deposited unit
A: SINGLE CHAIN FV
C: SINGLE CHAIN FV
P: P-GLYCOPROTEIN
Q: P-GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)61,7924
Polymers61,7924
Non-polymers00
Water1,15364
1
A: SINGLE CHAIN FV
P: P-GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)30,8962
Polymers30,8962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-6 kcal/mol
Surface area11230 Å2
MethodPISA
2
C: SINGLE CHAIN FV
Q: P-GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)30,8962
Polymers30,8962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-2 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.792, 82.659, 93.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.85727, -0.48481, -0.17336), (-0.48038, 0.63198, 0.60814), (-0.18527, 0.60462, -0.77467)
Vector: 70.78049, 77.66973, 70.08449)

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Components

#1: Antibody SINGLE CHAIN FV


Mass: 29321.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cellular location: PERIPLASMIC / Plasmid: PSJF2 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: Q6KB05, UniProt: Q505N9
#2: Protein/peptide P-GLYCOPROTEIN / EPITOPE PEPTIDE


Mass: 1574.757 Da / Num. of mol.: 2 / Fragment: ATP-BINDING DOMAIN / Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. / Source: (synth.) Cricetulus griseus (Chinese hamster)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 45 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.3
Details: THE PROTEIN WAS CRYSTALLIZED IN 40% MPD, 50 MM MES PH 6.3
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 %(v/v)MPD1drop
250 mMMES1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1999 / Details: MIRRORS
RadiationMonochromator: QUARTZ CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 21637 / % possible obs: 98.7 % / Redundancy: 15.1 % / Rsym value: 0.084 / Net I/σ(I): 23.1
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.472 / % possible all: 88.8
Reflection
*PLUS
Num. measured all: 142245 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 88.8 % / Num. unique obs: 1267 / Num. measured obs: 5585 / Rmerge(I) obs: 0.472

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AP2

1ap2


Resolution: 2.4→50 Å / Isotropic thermal model: RESTRAINED (GAUSSIAN) / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2047 9.5 %RANDOM
Rwork0.2207 ---
obs-20625 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.02 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso mean: 35.69 Å2
Baniso -1Baniso -2Baniso -3
1-9.569 Å20 Å20 Å2
2---0.23 Å20 Å2
3----9.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.35 Å
Luzzati sigma a0.5 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3890 0 0 64 3954
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.186
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.76
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.684
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.2991.5
X-RAY DIFFRACTIONx_mcangle_it4.8161.5
X-RAY DIFFRACTIONx_scbond_it5.1612
X-RAY DIFFRACTIONx_scangle_it6.5782
LS refinement shellResolution: 2.4→2.49 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3565 182 8.6 %
Rwork0.3595 1517 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 9.5 % / Rfactor obs: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.76
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.684
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it1.5
X-RAY DIFFRACTIONc_scangle_it2
LS refinement shell
*PLUS
% reflection Rfree: 8.6 %

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