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

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Basic information

Entry
Database: PDB / ID: 5xcq
TitleCrystal structure of P20.1 Fv-clasp fragment with its antigen peptide
Components
  • C8 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: 1.313 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: C8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6198
Polymers38,1393
Non-polymers4805
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-104 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.870, 89.230, 50.980
Angle α, β, γ (deg.)90.00, 108.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody VH-SARAH(Y35C)chimera


Mass: 19116.740 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: 18148.316 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-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.: 392 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M Bis-Tris (pH 5.5), 0.2 M Ammonium Sulfate, 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: Oct 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.31→48.48 Å / Num. obs: 84444 / % possible obs: 99.7 % / Redundancy: 7.5 % / Rsym value: 0.07 / Net I/σ(I): 16.91
Reflection shellResolution: 1.31→1.39 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 3.13 / Rsym value: 0.71 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2341: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZPK, 4NR2

2zpk

4nr2


Resolution: 1.313→39.818 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.23
RfactorNum. reflection% reflection
Rfree0.1817 4242 5.02 %
Rwork0.1651 --
obs0.1659 84437 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.313→39.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 25 392 3025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122900
X-RAY DIFFRACTIONf_angle_d1.2653982
X-RAY DIFFRACTIONf_dihedral_angle_d18.7431079
X-RAY DIFFRACTIONf_chiral_restr0.1434
X-RAY DIFFRACTIONf_plane_restr0.009522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3132-1.32810.29741390.25162471X-RAY DIFFRACTION94
1.3281-1.34370.24461290.23062717X-RAY DIFFRACTION100
1.3437-1.36010.26031320.22132626X-RAY DIFFRACTION100
1.3601-1.37730.24211480.21232687X-RAY DIFFRACTION100
1.3773-1.39550.23851340.20352717X-RAY DIFFRACTION100
1.3955-1.41460.20631430.2052641X-RAY DIFFRACTION100
1.4146-1.43480.22081430.19632666X-RAY DIFFRACTION100
1.4348-1.45620.23391500.19532691X-RAY DIFFRACTION100
1.4562-1.4790.20751240.19472649X-RAY DIFFRACTION100
1.479-1.50320.21511620.18642659X-RAY DIFFRACTION100
1.5032-1.52910.17621340.1822672X-RAY DIFFRACTION100
1.5291-1.55690.19771400.17162712X-RAY DIFFRACTION100
1.5569-1.58690.1691390.16952656X-RAY DIFFRACTION100
1.5869-1.61930.19531480.16282672X-RAY DIFFRACTION100
1.6193-1.65450.21861550.16622667X-RAY DIFFRACTION100
1.6545-1.6930.1941480.16072677X-RAY DIFFRACTION100
1.693-1.73530.19551400.16052670X-RAY DIFFRACTION100
1.7353-1.78220.1971240.16122674X-RAY DIFFRACTION100
1.7822-1.83470.19161520.16152701X-RAY DIFFRACTION100
1.8347-1.89390.18441370.16132692X-RAY DIFFRACTION100
1.8939-1.96160.18591600.1592632X-RAY DIFFRACTION100
1.9616-2.04010.17451330.15452715X-RAY DIFFRACTION100
2.0401-2.1330.16321330.15532675X-RAY DIFFRACTION100
2.133-2.24540.16021500.15672661X-RAY DIFFRACTION100
2.2454-2.38610.18161460.16232690X-RAY DIFFRACTION100
2.3861-2.57030.19181360.16412695X-RAY DIFFRACTION100
2.5703-2.82890.17771320.16582710X-RAY DIFFRACTION100
2.8289-3.23810.19061570.17332690X-RAY DIFFRACTION100
3.2381-4.0790.15861380.14762695X-RAY DIFFRACTION100
4.079-39.83680.14141360.14842715X-RAY DIFFRACTION99
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)
12.4277-0.57420.6241.6718-0.15920.8408-0.0701-0.00370.03050.2070.077-0.02810.01250.0304-0.00810.08080.0146-0.00550.0693-0.00740.0598-18.4252-21.25923.7806
22.8662-4.67070.04557.4435-0.20090.1174-0.1153-0.0510.37410.31740.0484-0.6545-0.0386-0.02290.05440.14370.0031-0.00110.1335-0.00980.13681.9355-13.865120.1148
31.07920.80760.18523.05520.30260.79820.03840.050.0136-0.03180.0326-0.1058-0.01030.0282-0.07020.06470.00220.00730.07930.00550.0664-14.5658-2.8244-8.1053
41.3266-3.7370.39517.5133-1.6774-0.0453-0.0581-0.0502-0.15350.12670.11050.313-0.0049-0.0377-0.04390.22460.035-0.05340.1408-0.02230.1384-7.928-7.469816.3852
50.85551.9135-1.08267.9754-7.39988.76060.14710.47210.0655-0.22330.27230.6229-0.2266-0.7485-0.36430.0981-0.0085-0.03740.15660.02360.1305-29.6025-16.6033-9.4172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 3:118))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 119:163))
3X-RAY DIFFRACTION3chain 'B' and ((resseq 4:113))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 114:158))
5X-RAY DIFFRACTION5chain 'C' and ((resseq 3:8))

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