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- PDB-1qok: MFE-23 AN ANTI-CARCINOEMBRYONIC ANTIGEN SINGLE-CHAIN FV ANTIBODY -

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Basic information

Entry
Database: PDB / ID: 1qok
TitleMFE-23 AN ANTI-CARCINOEMBRYONIC ANTIGEN SINGLE-CHAIN FV ANTIBODY
ComponentsMFE-23 RECOMBINANT ANTIBODY FRAGMENT
KeywordsIMMUNOGLOBULIN / SINGLE-CHAIN FV / ANTI-CARCINOEMBRYONIC ANTIGEN
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Anti-VIPase light chain variable region
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBoehm, M.K. / Corper, A.L. / Wan, T. / Sohi, M.K. / Sutton, B.J. / Thornton, J.D. / Keep, P.A. / Chester, K.A. / Begent, R.H.J. / Perkins, S.J.
CitationJournal: Biochem.J. / Year: 2000
Title: Crystal Structure of the Anti-Carcinoembryonic Antigen Single-Chain Fv Antibody Mfe-23 and a Model for Antigen Binding Based on Intermolecular Contacts
Authors: Boehm, M.K. / Corper, A.L. / Wan, T. / Sohi, M.K. / Sutton, B.J. / Thornton, J.D. / Keep, P.A. / Chester, K.A. / Begent, R.H.J. / Perkins, S.J.
History
DepositionNov 11, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.temp
Revision 1.5May 29, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.6Sep 25, 2019Group: Data collection / Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_sf
Revision 1.7Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
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: MFE-23 RECOMBINANT ANTIBODY FRAGMENT


Theoretical massNumber of molelcules
Total (without water)29,8751
Polymers29,8751
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.700, 61.700, 128.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody MFE-23 RECOMBINANT ANTIBODY FRAGMENT


Mass: 29874.986 Da / Num. of mol.: 1 / Fragment: SINGLE-CHAIN FV
Source method: isolated from a genetically manipulated source
Details: ANTI-CARCINOEMBRYONIC ANTIGEN SINGLE-CHAIN FRAGMENT CONTAINING AN N-TERMINAL VH DOMAIN LINKED BY A 3 (4GLY-SER) LINKER TO A VL DOMAIN AND A C-TERMINAL MYC TAG
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PUC119 / Cellular location (production host): EXTRACELLULAR / Production host: ESCHERICHIA COLI (E. coli) / References: GenBank: 2299568, UniProt: Q8K1F2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSUBDIVISION OF CHAIN: A (C=CHAIN IDENTIFIER; RES1=START RESIDUE; RES1=END RESIDUE;A=ALT CHAIN ...SUBDIVISION OF CHAIN: A (C=CHAIN IDENTIFIER; RES1=START RESIDUE; RES1=END RESIDUE;A=ALT CHAIN IDENTIFIER) C RES1 RES2 A A 27 146 H IMMUNOGLOBULIN VH FRAGMENT A 147 161 LINKER A 162 270 L IMMUNOGLOBULIN VL FRAGMENT A 271 282 C-TERMINAL MYC TAG
Sequence detailsMFE-23 IS A RECOMBINANT PROTEIN THAT WAS PRODUCED FROM THE RANDOM COMBINATION OF A MOUSE VH AND VL ...MFE-23 IS A RECOMBINANT PROTEIN THAT WAS PRODUCED FROM THE RANDOM COMBINATION OF A MOUSE VH AND VL IMMUNOGLOBULIN DOMAINS IN A PHAGE DISPLAY LIBRARY. THE SEQUENCE IS PUBLISHED IN INTERNATIONAL PATENT APPLICATION PCT/GB94/02658.

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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: 2.24 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: CRYSTALS WERE GROWN BY THE HANGING-DROP VAPOUR DIFFUSION METHOD AT 18 DEGREES (CELSIUS). PROTEIN SOLUTION (2 MG/ML) WAS MIXED 1:1 WITH 100 MM TRIS-HCL (PH6.5) CONTAINING 45% SATURATED ...Details: CRYSTALS WERE GROWN BY THE HANGING-DROP VAPOUR DIFFUSION METHOD AT 18 DEGREES (CELSIUS). PROTEIN SOLUTION (2 MG/ML) WAS MIXED 1:1 WITH 100 MM TRIS-HCL (PH6.5) CONTAINING 45% SATURATED AMMONIUM SULPHATE. A 10 UL DROPLET OF THIS MIXTURE WAS EQULIBRATED AGAINST 0.5 ML 100 MM TRIS-HCL (PH6.5) IN 45% AMMONIUM SULPHATE., pH 6.50
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mg/mlprotein1drop
250 mMTris-HCl1drop
322.5 %satammonium sulfate1drop
4100 mMTris-HCl1reservoir
545 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: R-AXIS II / Detector: IMAGE PLATE / Date: Mar 15, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 11539 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 5.3 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 4.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 3.2 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 1613

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FBJ

2fbj


Resolution: 2.4→8 Å / Rfactor Rfree error: 0.009
Cross valid method: THROUGHOUT EXCEPT FOR FINAL REFINEMENT CYCLE
σ(F): 2
Details: IN THE FINAL REFINEMENT CYCLE, THE WORKING AND TEST SETS WERE MERGED. AFTER THIS REFINEMENT, THE MODEL HAD AN R-FACTOR OF 19.0% AGAINST ALL REFLECTIONS BETWEEN 8.0 AND 2.4 ANGSTROMS..
RfactorNum. reflection% reflectionSelection details
Rfree0.267 933 8.1 %RANDOM
Rwork0.205 ---
obs0.205 11509 100 %-
Displacement parametersBiso mean: 25.1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 0 96 1827
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.68
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.32
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
LS refinement shellResolution: 2.4→2.48 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.4 85 7.8 %
Rwork0.325 1007 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 11204 / Num. reflection Rfree: 909 / % reflection Rfree: 8.5 % / Rfactor all: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.32
LS refinement shell
*PLUS
Rfactor Rfree: 0.4

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