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- PDB-5xcx: Crystal structure of TS2/16 Fv-clasp fragment -

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Basic information

Entry
Database: PDB / ID: 5xcx
TitleCrystal structure of TS2/16 Fv-clasp fragment
Components
  • VH(S112C)-SARAH Chimera
  • VL-SARAH(S37C) Chimera
KeywordsIMMUNE SYSTEM / antibody fragment / Fv-clasp
Function / homologyp53, subunit A / p53-like tetramerisation domain / Few Secondary Structures / Irregular / PHOSPHATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: VH(S112C)-SARAH Chimera
B: VL-SARAH(S37C) Chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5548
Polymers37,7352
Non-polymers8206
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-58 kcal/mol
Surface area16880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.200, 69.200, 171.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody VH(S112C)-SARAH Chimera


Mass: 19463.992 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(S37C) Chimera


Mass: 18270.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ?
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 177 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 1.2M NaH2PO4/0.8M K2HPO4, 0.1M CAPS (pH10.5), 0.2M Li2SO4

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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: Sep 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.04→47.05 Å / Num. obs: 27142 / % possible obs: 99.6 % / Redundancy: 15.8 % / Rsym value: 0.129 / Net I/σ(I): 18.42
Reflection shellResolution: 2.04→2.17 Å / Redundancy: 15.9 % / Mean I/σ(I) obs: 3.94 / Rsym value: 0.967 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→47.05 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.632 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.157 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22711 1306 4.8 %RANDOM
Rwork0.19412 ---
obs0.19574 25835 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.934 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.2 Å2
Refinement stepCycle: 1 / Resolution: 2.04→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 49 171 2826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022723
X-RAY DIFFRACTIONr_bond_other_d0.0020.022548
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.9863682
X-RAY DIFFRACTIONr_angle_other_deg0.89635918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7975335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.48924.248113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32115485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.621515
X-RAY DIFFRACTIONr_chiral_restr0.080.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022991
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02584
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_it0.5992.0821328
X-RAY DIFFRACTIONr_mcbond_other0.5982.0811327
X-RAY DIFFRACTIONr_mcangle_it1.033.1141658
X-RAY DIFFRACTIONr_mcangle_other1.033.1151659
X-RAY DIFFRACTIONr_scbond_it0.7622.2371392
X-RAY DIFFRACTIONr_scbond_other0.7592.2371392
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2543.3092021
X-RAY DIFFRACTIONr_long_range_B_refined3.6824.3472967
X-RAY DIFFRACTIONr_long_range_B_other3.67924.3422967
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.044→2.097 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 101 -
Rwork0.259 1746 -
obs--94.23 %
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)
11.23390.0963-0.92260.6185-0.07161.0029-0.0880.1858-0.06160.04490.00350.03250.0374-0.13620.08450.0989-0.05430.03040.1596-0.03520.0196-4.82734.322-23.011
20.81930.15850.10150.51730.88591.5812-0.04220.0418-0.01010.04750.0687-0.01910.07980.0599-0.02650.1089-0.00430.02280.1194-0.00670.014311.79741.396-10.623
33.91325.10491.30677.26612.16510.87890.0765-0.1150.34330.3057-0.15630.46030.13160.01240.07990.12970.01060.04950.09830.0070.0747-18.76342.7614.609
46.33126.99571.80667.83182.02120.8697-0.07290.21770.07690.02740.19050.1169-0.02120.0702-0.11760.1325-0.00560.05030.0921-0.00650.0711-10.94245.138-1.178
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 121
2X-RAY DIFFRACTION2B5 - 113
3X-RAY DIFFRACTION3A122 - 164
4X-RAY DIFFRACTION4B114 - 159

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