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

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Basic information

Entry
Database: PDB / ID: 5xcr
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: 1.75 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

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Assembly

Deposited unit
A: VH-SARAH(Y35C) chimera
B: VL-SARAH(M24C) chimera
C: C8 peptide
D: VH-SARAH(Y35C) chimera
E: VL-SARAH(M24C) chimera
F: C8 peptide


Theoretical massNumber of molelcules
Total (without water)76,2786
Polymers76,2786
Non-polymers00
Water9,422523
1
A: VH-SARAH(Y35C) chimera
B: VL-SARAH(M24C) chimera
C: C8 peptide


Theoretical massNumber of molelcules
Total (without water)38,1393
Polymers38,1393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-47 kcal/mol
Surface area16480 Å2
MethodPISA
2
D: VH-SARAH(Y35C) chimera
E: VL-SARAH(M24C) chimera
F: C8 peptide


Theoretical massNumber of molelcules
Total (without water)38,1393
Polymers38,1393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-45 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.060, 80.660, 85.700
Angle α, β, γ (deg.)90.00, 90.92, 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.: 2
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)
#2: Antibody VL-SARAH(M24C) chimera


Mass: 18148.316 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 C8 peptide


Mass: 873.976 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M Citrate (pH 5.5), 20%(w/v) PEG3000

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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: 1.75→46.66 Å / Num. obs: 75053 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rsym value: 0.09 / Net I/σ(I): 16.69
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 3.22 / Rsym value: 0.71 / % possible all: 99.2

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Processing

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

5xcq


Resolution: 1.75→46.66 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.43 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20224 3806 5.1 %RANDOM
Rwork0.17075 ---
obs0.17235 71247 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.234 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å2-0.09 Å2
2--0.58 Å20 Å2
3----0.23 Å2
Refinement stepCycle: 1 / Resolution: 1.75→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5209 0 0 523 5732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.025440
X-RAY DIFFRACTIONr_bond_other_d0.0020.024946
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9497408
X-RAY DIFFRACTIONr_angle_other_deg0.9433.00211520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7025.015684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11124.73241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28915925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0621528
X-RAY DIFFRACTIONr_chiral_restr0.0910.2818
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216088
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021096
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_it0.8981.4722711
X-RAY DIFFRACTIONr_mcbond_other0.8971.4722710
X-RAY DIFFRACTIONr_mcangle_it1.5342.1993401
X-RAY DIFFRACTIONr_mcangle_other1.5342.1993402
X-RAY DIFFRACTIONr_scbond_it1.1441.6382729
X-RAY DIFFRACTIONr_scbond_other1.1441.6382729
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8632.3884007
X-RAY DIFFRACTIONr_long_range_B_refined4.67318.2626146
X-RAY DIFFRACTIONr_long_range_B_other4.51917.7256044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.753→1.799 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 289 -
Rwork0.224 5139 -
obs--98.32 %
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)
10.80180.14940.74220.4329-0.05072.2604-0.0581-0.07050.0267-0.0407-0.0164-0.0198-0.0413-0.0950.07450.01920.0307-0.00320.0846-0.03760.033919.168-12.06917.663
23.072-0.3640.05711.0232-0.23651.9211-0.0861-0.47180.04590.073-0.00010.00910.0308-0.16790.08620.01210.0267-0.00240.1947-0.03690.009310.862-18.82236.871
315.65215.0005-1.26119.6989-2.85879.2101-0.102-0.0138-0.64810.06240.0296-0.81550.20280.34690.07240.04030.05430.01120.10880.00360.09125.888-25.90530.779
41.22220.1174-0.26421.1212-1.11522.6321-0.0407-0.0666-0.08210.14490.05040.0134-0.1-0.1717-0.00970.08520.0120.02420.06020.0220.016444.0167.36424.329
51.16060.01070.1230.9627-0.35421.8395-0.0496-0.0009-0.03580.09190.05780.0441-0.0175-0.188-0.00820.04220.00470.01840.06250.01250.010935.48117.7756.422
68.7682-5.2218-1.175817.4723-3.87873.9303-0.1710.1130.01550.0384-0.2895-1.0575-0.03460.41560.46050.0615-0.0236-0.0190.08650.04780.096454.37618.94110.818
71.0255-0.7293-2.5240.8331.99557.0546-0.0814-0.0967-0.06920.07630.0769-0.0040.19860.29120.00450.0110.02570.00090.1176-0.02610.0428-6.213-18.94627.039
81.5416-1.698-4.12872.60864.77611.65290.0790.0304-0.00390.00580.039-0.02-0.1052-0.026-0.1180.0330.028-0.01480.0814-0.01290.0409-14.419-11.86429.484
91.47961.41533.40382.05083.40577.8805-0.11460.0989-0.0215-0.0910.1593-0.0035-0.27250.2141-0.04460.0273-0.01680.00640.1519-0.00630.00818.21615.63614.728
100.88981.14051.50381.88362.40734.79580.06210.0301-0.07010.03620.103-0.05420.10790.0127-0.16510.04870.01350.00160.06180.00190.030210.2898.56214.517
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E2 - 115
2X-RAY DIFFRACTION2D3 - 120
3X-RAY DIFFRACTION3F3 - 8
4X-RAY DIFFRACTION4B4 - 115
5X-RAY DIFFRACTION5A3 - 120
6X-RAY DIFFRACTION6C2 - 8
7X-RAY DIFFRACTION7E116 - 158
8X-RAY DIFFRACTION8D121 - 163
9X-RAY DIFFRACTION9B116 - 158
10X-RAY DIFFRACTION10A121 - 163

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