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- PDB-5xct: Crystal structure of P20.1 Fv-clasp fragment with its antigen peptide -

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Basic information

Entry
Database: PDB / ID: 5xct
TitleCrystal structure of P20.1 Fv-clasp fragment with its antigen peptide
Components
  • C8 peptide
  • 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 / 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: 1.17 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VH(S112C)-SARAH chimera
B: VL-SARAH(S37C)chimera
C: C8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0854
Polymers38,0493
Non-polymers351
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-55 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.100, 55.159, 62.484
Angle α, β, γ (deg.)90.00, 93.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody VH(S112C)-SARAH chimera


Mass: 19109.785 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: 18065.332 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 C8 peptide


Mass: 873.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M Bis-Tris (pH 6.5), 20%(w/v) PEG3350

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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: 1.17→50 Å / Num. obs: 109121 / % possible obs: 97 % / Redundancy: 4.2 % / Rsym value: 0.053 / Net I/σ(I): 17.77
Reflection shellResolution: 1.17→1.19 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.45 / Rsym value: 0.54 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2341: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XCQ

5xcq


Resolution: 1.17→27.579 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.33
RfactorNum. reflection% reflection
Rfree0.1849 5434 4.98 %
Rwork0.152 --
obs0.1536 109090 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.17→27.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 1 448 3085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072997
X-RAY DIFFRACTIONf_angle_d0.9294110
X-RAY DIFFRACTIONf_dihedral_angle_d25.0051146
X-RAY DIFFRACTIONf_chiral_restr0.087443
X-RAY DIFFRACTIONf_plane_restr0.006546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1688-1.18210.21671580.22983031X-RAY DIFFRACTION86
1.1821-1.1960.22881830.22083240X-RAY DIFFRACTION91
1.196-1.21060.2611650.21393298X-RAY DIFFRACTION93
1.2106-1.22590.23161970.20733330X-RAY DIFFRACTION94
1.2259-1.2420.23841800.20163332X-RAY DIFFRACTION95
1.242-1.2590.23222050.19883402X-RAY DIFFRACTION95
1.259-1.2770.21472000.19463358X-RAY DIFFRACTION96
1.277-1.29610.21451860.18143457X-RAY DIFFRACTION97
1.2961-1.31630.21131700.18433408X-RAY DIFFRACTION96
1.3163-1.33790.21451820.17693435X-RAY DIFFRACTION97
1.3379-1.3610.20231800.16813459X-RAY DIFFRACTION97
1.361-1.38570.2121970.1623428X-RAY DIFFRACTION97
1.3857-1.41240.20281810.15873441X-RAY DIFFRACTION97
1.4124-1.44120.20751720.15423497X-RAY DIFFRACTION98
1.4412-1.47250.19131940.15333429X-RAY DIFFRACTION98
1.4725-1.50680.191480.15013528X-RAY DIFFRACTION98
1.5068-1.54450.16631620.14423499X-RAY DIFFRACTION98
1.5445-1.58620.17381670.14193532X-RAY DIFFRACTION98
1.5862-1.63290.18281860.14043495X-RAY DIFFRACTION98
1.6329-1.68560.19421860.1413494X-RAY DIFFRACTION98
1.6856-1.74580.17151780.14243511X-RAY DIFFRACTION99
1.7458-1.81570.18362140.14723490X-RAY DIFFRACTION99
1.8157-1.89830.15691940.14783550X-RAY DIFFRACTION99
1.8983-1.99840.17151820.14543512X-RAY DIFFRACTION99
1.9984-2.12360.17191640.15163582X-RAY DIFFRACTION99
2.1236-2.28740.18761610.15263576X-RAY DIFFRACTION100
2.2874-2.51750.18712060.15243561X-RAY DIFFRACTION100
2.5175-2.88140.18091940.1533598X-RAY DIFFRACTION100
2.8814-3.6290.18111840.14483600X-RAY DIFFRACTION100
3.629-27.58720.17021580.13643583X-RAY DIFFRACTION97

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