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- PDB-3wfh: Crystal structure of anti-Prostaglandin E2 Fab fragment PGE2 complex -

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Basic information

Entry
Database: PDB / ID: 3wfh
TitleCrystal structure of anti-Prostaglandin E2 Fab fragment PGE2 complex
Components
  • mAb Fab H fragment
  • mAb Fab L fragment
KeywordsIMMUNE SYSTEM / immunogloblin / Anti-Prostaglandin E2 antibody / prostaglandin E2 / Fab fragment by papain digestion
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-P2E
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSugahara, M. / Ago, H. / Saino, H. / Miyano, M.
CitationJournal: To be Published
Title: Crystal structure of anti-Prostaglandin E2 Fab fragment with Prostaglandin E2
Authors: Sugahara, M. / Ago, H. / Saino, H. / Miyano, M. / Kurahashi, Y. / Aoyama, S. / Takehira, M. / Yutani, K. / Yamamoto, S.
History
DepositionJul 19, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mAb Fab H fragment
B: mAb Fab L fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5283
Polymers47,1762
Non-polymers3521
Water10,287571
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-26 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.260, 82.530, 82.740
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 mAb Fab H fragment


Mass: 23396.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: Hybridoma
#2: Antibody mAb Fab L fragment


Mass: 23779.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: Hybridoma
#3: Chemical ChemComp-P2E / (Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid / Prostaglandin E2


Mass: 352.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE REFERENCE SEQUENCE OF CHAIN A IS BAL50003 AND CHAIN B IS BAL50004 IN GENBANK.

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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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 293 K / Method: oil microbatch / pH: 6
Details: 30%(w/v) PEG 4000, 0.2M ammonium sulfate, 0.1M Na-citrate, pH 6.0, OIL MICROBATCH, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 25, 2009
RadiationMonochromator: SI(111) DOUBL CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→35.13 Å / Num. obs: 38574 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.138
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 4.4 / Num. unique all: 5547 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DDQ

2ddq


Resolution: 1.9→35.13 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8948 / SU ML: 0.17 / σ(F): 1.35 / Phase error: 17.26 / Stereochemistry target values: ML / Details: The structure was refined also REFMAC5 and CNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 1928 5 %RANDOM
Rwork0.1676 ---
obs0.1691 38569 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.97 Å2 / Biso mean: 22.1638 Å2 / Biso min: 3.85 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 25 571 3838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053436
X-RAY DIFFRACTIONf_angle_d1.0064690
X-RAY DIFFRACTIONf_chiral_restr0.069530
X-RAY DIFFRACTIONf_plane_restr0.005601
X-RAY DIFFRACTIONf_dihedral_angle_d12.4151200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.96790.26022070.201435883795
1.9679-2.04670.21351830.1836053788
2.0467-2.13980.18941770.173436193796
2.1398-2.25260.23641860.173636483834
2.2526-2.39370.19251790.17936343813
2.3937-2.57850.2282260.179236203846
2.5785-2.83790.21972000.179236493849
2.8379-3.24830.18661890.168236763865
3.2483-4.09150.20051940.150137143908
4.0915-35.1360.1571870.154638884075

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