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- PDB-5xcs: Crystal structure of 12CA5 Fv-clasp fragment with its antigen peptide -

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Basic information

Entry
Database: PDB / ID: 5xcs
TitleCrystal structure of 12CA5 Fv-clasp fragment with its antigen peptide
Components
  • HA peptide
  • VH-SARAH(Y35C) chimera
  • VL-SARAH(M24C) chimera
KeywordsIMMUNE SYSTEM / antibody fragment / Fv-clasp
Function / homologyp53, subunit A / p53-like tetramerisation domain / Few Secondary Structures / Irregular / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsArimori, T. / Takagi, J.
CitationJournal: Structure / Year: 2017
Title: Fv-clasp: An Artificially Designed Small Antibody Fragment with Improved Production Compatibility, Stability, and Crystallizability
Authors: Arimori, T. / Kitago, Y. / Umitsu, M. / Fujii, Y. / Asaki, R. / Tamura-Kawakami, K. / Takagi, J.
History
DepositionMar 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: 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: VH-SARAH(Y35C) chimera
B: VL-SARAH(M24C) chimera
C: HA peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7598
Polymers39,2793
Non-polymers4805
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-104 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.870, 85.660, 76.540
Angle α, β, γ (deg.)90.00, 125.71, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

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Components

#1: Antibody VH-SARAH(Y35C) chimera


Mass: 19522.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli)
#2: Antibody VL-SARAH(M24C) chimera


Mass: 18654.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli)
#3: Protein/peptide HA peptide


Mass: 1102.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.18 Å3/Da / Density % sol: 61.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M Na/K phosphate pH6.2, 1.4M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→42.83 Å / Num. obs: 24599 / % possible obs: 98 % / Redundancy: 7.5 % / Rsym value: 0.14 / Net I/σ(I): 13.6
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 3.41 / Rsym value: 0.9 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HIL, 5XCQ

1hil

5xcq


Resolution: 2.2→38.11 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.626 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1280 5.2 %RANDOM
Rwork0.20817 ---
obs0.21005 23282 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20.02 Å2
2---3.8 Å20 Å2
3---2.26 Å2
Refinement stepCycle: 1 / Resolution: 2.2→38.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 25 89 2798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022761
X-RAY DIFFRACTIONr_bond_other_d0.0010.022493
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9753733
X-RAY DIFFRACTIONr_angle_other_deg0.92335819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9265334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3324.516124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31915490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8741516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213004
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02548
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9122.7221348
X-RAY DIFFRACTIONr_mcbond_other0.9122.7211347
X-RAY DIFFRACTIONr_mcangle_it1.534.0711678
X-RAY DIFFRACTIONr_mcangle_other1.534.0721679
X-RAY DIFFRACTIONr_scbond_it1.1412.8771413
X-RAY DIFFRACTIONr_scbond_other1.1162.8141394
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8634.1612026
X-RAY DIFFRACTIONr_long_range_B_refined4.10130.4732958
X-RAY DIFFRACTIONr_long_range_B_other3.65330.2872945
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.203→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 73 -
Rwork0.408 1389 -
obs--80.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.43221.1046-0.01681.22110.04160.63440.146-0.08440.07940.0576-0.16430.0768-0.0520.04910.01820.0675-0.0377-0.0650.1950.00170.1462-24.249-5.04711.823
20.52470.4579-0.29650.8869-0.66121.3181-0.00010.0245-0.0595-0.1516-0.0267-0.06560.1320.17510.02680.06170.0313-0.03940.20020.00650.1487-16.849-14.607-6.977
31.75921.10812.94040.73821.52618.0992-0.0585-0.13660.1608-0.0526-0.10260.0880.1323-0.2490.16110.03020.0092-0.04950.2168-0.01620.132-7.60817.201-5.774
42.75562.8066.62593.14987.053216.58360.1197-0.1840.18620.0796-0.32850.11870.3417-0.46510.20880.1-0.0337-0.06590.24090.01030.133-14.47912.181-1.439
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 122
2X-RAY DIFFRACTION2B4 - 117
3X-RAY DIFFRACTION3A123 - 161
4X-RAY DIFFRACTION4B122 - 159

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