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- PDB-5yfi: Crystal structure of the anti-human prostaglandin E receptor EP4 ... -

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Basic information

Entry
Database: PDB / ID: 5yfi
TitleCrystal structure of the anti-human prostaglandin E receptor EP4 antibody Fab fragment
Components
  • Heavy chain of Fab fragment
  • Light chain of Fab fragment
KeywordsIMMUNE SYSTEM / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.848 Å
AuthorsToyoda, Y. / Morimoto, K. / Suno, R. / Horita, S. / Iwata, S. / Kobayashi, T.
CitationJournal: Nat. Chem. Biol. / Year: 2019
Title: Ligand binding to human prostaglandin E receptor EP4at the lipid-bilayer interface.
Authors: Toyoda, Y. / Morimoto, K. / Suno, R. / Horita, S. / Yamashita, K. / Hirata, K. / Sekiguchi, Y. / Yasuda, S. / Shiroishi, M. / Shimizu, T. / Urushibata, Y. / Kajiwara, Y. / Inazumi, T. / ...Authors: Toyoda, Y. / Morimoto, K. / Suno, R. / Horita, S. / Yamashita, K. / Hirata, K. / Sekiguchi, Y. / Yasuda, S. / Shiroishi, M. / Shimizu, T. / Urushibata, Y. / Kajiwara, Y. / Inazumi, T. / Hotta, Y. / Asada, H. / Nakane, T. / Shiimura, Y. / Nakagita, T. / Tsuge, K. / Yoshida, S. / Kuribara, T. / Hosoya, T. / Sugimoto, Y. / Nomura, N. / Sato, M. / Hirokawa, T. / Kinoshita, M. / Murata, T. / Takayama, K. / Yamamoto, M. / Narumiya, S. / Iwata, S. / Kobayashi, T.
History
DepositionSep 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Light chain of Fab fragment
H: Heavy chain of Fab fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5818
Polymers54,1892
Non-polymers3926
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-171 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.703, 60.784, 200.182
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Light chain of Fab fragment


Mass: 26614.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Heavy chain of Fab fragment


Mass: 27574.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.17 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 4000, 200 mM zinc acetate, 100 mM MES (pH 6.5), 100 mM guanidine hydrochloride

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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: Apr 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.848→50 Å / Num. obs: 81114 / % possible obs: 98.8 % / Redundancy: 5.2 % / Net I/σ(I): 9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.848→44.935 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.7 / Phase error: 23.66
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2315 4067 5.01 %
Rwork0.1938 --
obs0.1957 81114 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.848→44.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3370 0 6 315 3691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053507
X-RAY DIFFRACTIONf_angle_d0.7664784
X-RAY DIFFRACTIONf_dihedral_angle_d11.4872101
X-RAY DIFFRACTIONf_chiral_restr0.051524
X-RAY DIFFRACTIONf_plane_restr0.004607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.848-1.86980.37461320.31922544X-RAY DIFFRACTION96
1.8698-1.89260.32551420.31632674X-RAY DIFFRACTION100
1.8926-1.91650.35211410.29952697X-RAY DIFFRACTION100
1.9165-1.94180.33561410.29112687X-RAY DIFFRACTION100
1.9418-1.96840.3171330.26872664X-RAY DIFFRACTION99
1.9684-1.99650.30291420.26112638X-RAY DIFFRACTION100
1.9965-2.02630.24871430.25572722X-RAY DIFFRACTION98
2.0263-2.0580.30191350.25572564X-RAY DIFFRACTION98
2.058-2.09170.3111450.25062712X-RAY DIFFRACTION100
2.0917-2.12780.26541390.24612691X-RAY DIFFRACTION100
2.1278-2.16640.27541460.22452676X-RAY DIFFRACTION100
2.1664-2.20810.25731420.22032698X-RAY DIFFRACTION100
2.2081-2.25320.2381420.22112683X-RAY DIFFRACTION100
2.2532-2.30220.31611380.20582656X-RAY DIFFRACTION99
2.3022-2.35570.25671390.20852685X-RAY DIFFRACTION100
2.3557-2.41460.25421430.21432694X-RAY DIFFRACTION100
2.4146-2.47990.26881380.20572619X-RAY DIFFRACTION99
2.4799-2.55290.24041440.21322709X-RAY DIFFRACTION99
2.5529-2.63530.2521350.19262583X-RAY DIFFRACTION97
2.6353-2.72950.22181470.18452693X-RAY DIFFRACTION99
2.7295-2.83870.231380.18112649X-RAY DIFFRACTION100
2.8387-2.96790.24051350.17722691X-RAY DIFFRACTION100
2.9679-3.12430.27141430.17952710X-RAY DIFFRACTION100
3.1243-3.320.21451460.18822660X-RAY DIFFRACTION100
3.32-3.57630.20531440.1672627X-RAY DIFFRACTION98
3.5763-3.9360.20541370.16072574X-RAY DIFFRACTION96
3.936-4.50510.17991430.14692665X-RAY DIFFRACTION98
4.5051-5.67410.15851370.13992596X-RAY DIFFRACTION97
5.6741-44.94860.17831370.17822586X-RAY DIFFRACTION96
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)
11.92160.1581-0.84552.5573-0.37192.98470.1015-0.2730.02210.5026-0.04810.0736-0.1321-0.0102-0.05290.2345-0.02380.00740.1723-0.01080.1539-3.791622.0954-30.4114
21.2658-0.0441-0.72611.2397-1.70872.82310.0371-0.17420.00310.09630.01160.26740.2309-0.1223-0.05580.4496-0.02030.07330.27920.00090.1755-17.9615-3.2395-14.3633
31.8212-0.2087-0.00187.6245-0.68943.66110.0767-0.2848-0.19030.7093-0.0758-0.19080.53730.21820.00210.49090.01910.01870.31580.03760.2234-14.8421-9.3561-10.2884
40.4068-1.61480.37668.8798-1.92251.08560.0379-0.0658-0.13880.06120.00840.4786-0.0531-0.0977-0.03780.10740.0022-0.00410.1645-0.00950.2065-16.02518.1884-48.5901
53.72680.4774-1.22683.4878-0.94985.692-0.0556-0.0958-0.13260.1351-0.0531-0.26750.04150.21090.09190.091-0.0109-0.02390.1172-0.02860.2112-2.851110.7996-46.6802
60.68830.4362-0.19772.0231-0.63681.33120.0411-0.0768-0.00880.1217-0.0798-0.0472-0.05760.06030.04830.10360.00930.00220.1417-0.01190.1612-11.89975.3148-43.8599
73.2001-0.6062-0.2873.4898-2.04893.0492-0.2283-0.8443-0.32460.8999-0.05430.44380.2475-0.49730.23730.4443-0.11990.12540.5294-0.0160.2675-27.2575-8.7668-13.6894
82.5594-0.016-0.11021.731.06574.1446-0.0527-0.43750.02470.333-0.13440.3387-0.0109-0.7890.10220.23360.01060.08760.3409-0.02210.2336-26.4334-5.859-23.7966
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 23 through 123 )
2X-RAY DIFFRACTION2chain 'L' and (resid 124 through 150 )
3X-RAY DIFFRACTION3chain 'L' and (resid 151 through 236 )
4X-RAY DIFFRACTION4chain 'H' and (resid 20 through 51 )
5X-RAY DIFFRACTION5chain 'H' and (resid 52 through 86 )
6X-RAY DIFFRACTION6chain 'H' and (resid 87 through 151 )
7X-RAY DIFFRACTION7chain 'H' and (resid 152 through 172 )
8X-RAY DIFFRACTION8chain 'H' and (resid 173 through 242 )

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