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- PDB-1ap2: SINGLE CHAIN FV OF C219 -

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Basic information

Entry
Database: PDB / ID: 1ap2
TitleSINGLE CHAIN FV OF C219
Components(MONOCLONAL ANTIBODY C219) x 2
KeywordsIMMUNOGLOBULIN / SINGLE CHAIN FV / MONOCLONAL ANTIBODY / C219 / P-GLYCOPROTEIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsHoedemaeker, P.J. / Rose, D.R.
CitationJournal: 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
DepositionJul 23, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MONOCLONAL ANTIBODY C219
B: MONOCLONAL ANTIBODY C219
C: MONOCLONAL ANTIBODY C219
D: MONOCLONAL ANTIBODY C219


Theoretical massNumber of molelcules
Total (without water)51,7394
Polymers51,7394
Non-polymers00
Water1,838102
1
A: MONOCLONAL ANTIBODY C219
B: MONOCLONAL ANTIBODY C219


Theoretical massNumber of molelcules
Total (without water)25,8702
Polymers25,8702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-13 kcal/mol
Surface area10430 Å2
MethodPISA
2
C: MONOCLONAL ANTIBODY C219
D: MONOCLONAL ANTIBODY C219


Theoretical massNumber of molelcules
Total (without water)25,8702
Polymers25,8702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-12 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.040, 64.350, 154.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.1273, 0.9916, 0.0212), (0.9907, -0.1282, 0.0461), (0.0484, 0.0151, -0.9987)10.2166, -12.8951, 36.5168
2given(0.1026, 0.9945, 0.0228), (0.9934, -0.1036, 0.0498), (0.0519, 0.0175, -0.9985)11.3214, -13.3462, 36.226

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Components

#1: Antibody MONOCLONAL ANTIBODY C219 / VARIABLE DOMAIN


Mass: 12296.612 Da / Num. of mol.: 2 / Fragment: FV
Source method: isolated from a genetically manipulated source
Details: LIGHT AND HEAVY CHAINS LINKED WITH A SYNTHETIC (GGGGS)3 LINKER
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CDNA / Plasmid: PSJF2 / Cellular location (production host): PERIPLASMIC / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: GenBank: 196573
#2: Antibody MONOCLONAL ANTIBODY C219 / VARIABLE DOMAIN


Mass: 13572.992 Da / Num. of mol.: 2 / Fragment: FV
Source method: isolated from a genetically manipulated source
Details: LIGHT AND HEAVY CHAINS LINKED WITH A SYNTHETIC (GGGGS)3 LINKER
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CDNA / Plasmid: PSJF2 / Cellular location (production host): PERIPLASMIC / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: EMBL: Z22078
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
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: 2.85 Å3/Da / Density % sol: 58 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.5
Details: THE PROTEIN WAS CRYSTALLIZED IN 21% PEG 6000, 100 MM SODIUM CITRATE PH 4.5, IN HANGING DROPS CONTAINING SUBTILISIN CARLSBERG IN A 1:100 MOLAR RATIO., vapor diffusion - hanging drop THE ...Details: THE PROTEIN WAS CRYSTALLIZED IN 21% PEG 6000, 100 MM SODIUM CITRATE PH 4.5, IN HANGING DROPS CONTAINING SUBTILISIN CARLSBERG IN A 1:100 MOLAR RATIO., vapor diffusion - hanging drop THE DEPOSITORS CRYSTALLIZED THE SINGLE CHAIN FV IN THE PRESENCE OF SUBTILISIN, AS DESCRIBED IN THE PRIMARY REFERENCE. THE SEQUENCE OF THE SINGLE CHAIN IS DIVMTQSPSSLTVTAGEKVTMSCKSSQSLLNSGNQKNYLTWYQQKPGQPPKLLIYWAS TRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQNDYSYPLTFGAGTKLEP (LIGHT CHAINS A AND C) GGGGSGGGGSGKSGGGG (LINKER) EVQLQQSGAELVRPGASVKLSCTASGFNIKDDFMHWVKQRPEQGLEWIGRIDPANDNT KYAPKFQDKATIIADTSSNTAYLQLSSLTSEDTAVYYCARREVYSYYSPLDVWGAGTT VTVPSG (HEAVY CHAINS B AND D) SEQKLISEEDLNHHHHH (C-MYC TAG + 5XHIS TAG) THE DEPOSITORS HAVE NOT DETERMINED WHERE SUBTILISIN CLEAVES EXACTLY, BUT THE MOBILITY ON SDS GELS SUGGESTS THAT THE MOST OF THE LINKER AND MOST OF BOTH TAGS ARE REMOVED.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
210 mMTris-HCl1drop
3100 mMsodium citrate1reservoir
421 %(w/v)PEG60001reservoir
5subtilisin1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: May 1, 1997
RadiationMonochromator: QUARTZ CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. obs: 22616 / % possible obs: 91.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rsym value: 0.098 / Net I/σ(I): 9.7
Reflection shellResolution: 2.36→2.55 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.277 / % possible all: 76.1
Reflection
*PLUS
Num. measured all: 81247 / Rmerge(I) obs: 0.098
Reflection shell
*PLUS
% possible obs: 76.1 % / Num. unique obs: 3671 / Num. measured obs: 8466 / Rmerge(I) obs: 0.277

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Processing

Software
NameVersionClassification
SDMSdata collection
SDMSdata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
SDMSdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IGM

1igm


Resolution: 2.36→6 Å / Rfactor Rfree error: 0.0073 / Data cutoff high absF: 10000000 / Data cutoff low absF: 3 / Isotropic thermal model: RESTRAINED (GAUSSIAN) / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1519 7.8 %RANDOM
Rwork0.2045 ---
obs0.2045 19352 78.4 %-
Displacement parametersBiso mean: 10.77 Å2
Refinement stepCycle: LAST / Resolution: 2.36→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 0 102 3722
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.121
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30.29
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.572
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it6.3431.5
X-RAY DIFFRACTIONx_mcangle_it8.011.5
X-RAY DIFFRACTIONx_scbond_it2.9572
X-RAY DIFFRACTIONx_scangle_it2.9312
LS refinement shellResolution: 2.36→2.46 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3798 91 7.6 %
Rwork0.2584 1109 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.206 / Rfactor Rfree: 0.285
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.11
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30.26
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.572
LS refinement shell
*PLUS
Rfactor Rfree: 0.373 / Rfactor obs: 0.2582

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