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

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Basic information

Entry
Database: PDB / ID: 5xcu
TitleCrystal structure of 12CA5 Fv-clasp fragment with its antigen peptide
Components
  • HA peptide
  • VH(S112C)-SARAH chimera,VH(S112C)-SARAH chimera
  • VL-SARAH(S37C) 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: 2.454 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 9, 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(S112C)-SARAH chimera,VH(S112C)-SARAH chimera
B: VL-SARAH(S37C) chimera,VL-SARAH(S37C) chimera
C: HA peptide
D: VH(S112C)-SARAH chimera,VH(S112C)-SARAH chimera
E: VL-SARAH(S37C) chimera,VL-SARAH(S37C) chimera
F: HA peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9918
Polymers78,7996
Non-polymers1922
Water2,720151
1
A: VH(S112C)-SARAH chimera,VH(S112C)-SARAH chimera
B: VL-SARAH(S37C) chimera,VL-SARAH(S37C) chimera
C: HA peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4954
Polymers39,3993
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-59 kcal/mol
Surface area16750 Å2
MethodPISA
2
D: VH(S112C)-SARAH chimera,VH(S112C)-SARAH chimera
E: VL-SARAH(S37C) chimera,VL-SARAH(S37C) chimera
F: HA peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4954
Polymers39,3993
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-49 kcal/mol
Surface area16790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.380, 107.310, 66.700
Angle α, β, γ (deg.)90.00, 92.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody VH(S112C)-SARAH chimera,VH(S112C)-SARAH chimera


Mass: 19598.133 Da / Num. of mol.: 2
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,VL-SARAH(S37C) chimera


Mass: 18699.033 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2M Ammonium sulfate, 0.1M HEPES (pH 7.5), 25%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→44.58 Å / Num. obs: 29296 / % possible obs: 98.9 % / Redundancy: 5.2 % / Rsym value: 0.12 / Net I/σ(I): 10.85
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.49 / Rsym value: 0.64 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XCS

5xcs


Resolution: 2.454→44.58 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 1466 5.01 %
Rwork0.1987 --
obs0.2011 29290 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.454→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5360 0 10 151 5521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085482
X-RAY DIFFRACTIONf_angle_d0.9597412
X-RAY DIFFRACTIONf_dihedral_angle_d7.9333316
X-RAY DIFFRACTIONf_chiral_restr0.05800
X-RAY DIFFRACTIONf_plane_restr0.005946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4538-2.54150.34491460.26752759X-RAY DIFFRACTION99
2.5415-2.64320.33871480.25962797X-RAY DIFFRACTION99
2.6432-2.76350.33261450.27032769X-RAY DIFFRACTION99
2.7635-2.90920.26971440.25972732X-RAY DIFFRACTION97
2.9092-3.09140.32651460.2412778X-RAY DIFFRACTION100
3.0914-3.330.29871480.23092807X-RAY DIFFRACTION100
3.33-3.6650.23581460.19092766X-RAY DIFFRACTION99
3.665-4.1950.19541460.17062778X-RAY DIFFRACTION99
4.195-5.28390.16441480.14012817X-RAY DIFFRACTION99
5.2839-44.5870.23531490.16942821X-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)
11.3454-0.0395-0.01291.7744-0.63520.8190.0763-0.1182-0.1117-0.0364-0.10760.07520.03960.01060.05390.188-0.0134-0.0130.2032-0.00920.213221.378519.514110.363
22.13511.8388-0.52272.7673-0.16980.67780.0308-0.0048-0.39080.0256-0.0697-0.33840.05930.04190.04590.35980.0258-0.01560.24490.00650.17741.966-3.66317.286
32.3113-1.031-0.38521.240.34550.923-0.06960.00470.0012-0.06260.0393-0.16930.02010.09690.02330.2166-0.0013-0.00390.2109-0.00540.274337.546422.9057-4.2399
41.8541.2249-0.57391.8125-0.24990.46940.4027-0.21160.22760.4031-0.21390.0902-0.18390.0646-0.12840.31420.0006-0.01880.21450.01210.229938.8745.68417.327
51.2198-0.12480.78881.1943-0.62832.4175-0.1004-0.1217-0.03460.07190.0997-0.1080.03260.3743-0.04850.27180.0290.01140.3901-0.010.262346.5812-1.963243.0862
63.9099-0.13211.86340.75190.02131.4590.1022-0.6190.05220.0892-0.0262-0.02140.0214-0.1547-0.02120.372-0.01440.04650.3254-0.00960.290730.318-10.79570.502
71.4952-0.2769-0.2881.4520.15052.3148-0.018-0.0530.0790.10910.12610.1846-0.2373-0.2254-0.11220.30130.03110.01760.29480.03630.296826.13535.369839.6381
81.63230.4750.4350.9774-0.2822.1986-0.0680.2837-0.0148-0.02180.10150.1801-0.10310.1654-0.08490.32660.02440.05590.19920.01270.293235.297-9.43362.348
93.779-0.1788-2.46661.91221.44596.51210.42630.47530.020.0862-0.58940.0986-0.7167-0.81250.09350.5050.00570.03350.32620.01930.224914.453833.80132.7597
101.53171.39592.17691.94380.9596.13330.0359-0.1990.51490.39180.6071-0.67130.50140.8589-0.62450.43710.0336-0.05030.3906-0.04830.37948.38973.052826.2473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1:120))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 121:164))
3X-RAY DIFFRACTION3chain 'B' and ((resseq 1:114))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 115:159))
5X-RAY DIFFRACTION5chain 'D' and ((resseq 1:120))
6X-RAY DIFFRACTION6chain 'D' and ((resseq 126:163))
7X-RAY DIFFRACTION7chain 'E' and ((resseq 2:119))
8X-RAY DIFFRACTION8chain 'E' and ((resseq 120:158))
9X-RAY DIFFRACTION9chain 'C'
10X-RAY DIFFRACTION10chain 'F'

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