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- PDB-3whx: Crystal structure of anti-prostaglandin E2 Fab fragment PGE1 complex -

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Basic information

Entry
Database: PDB / ID: 3whx
TitleCrystal structure of anti-prostaglandin E2 Fab fragment PGE1 complex
Components
  • mAb Fab H fragment
  • mAb Fab L fragment
KeywordsIMMUNE SYSTEM / immunogloblin / Anti-Prostaglandin E2 antibody / Prostaglandin E2
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-XPG
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
DepositionSep 3, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 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 1.2Oct 30, 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: mAb Fab H fragment
B: mAb Fab L fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7593
Polymers47,4052
Non-polymers3541
Water13,565753
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-28 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.460, 82.030, 82.310
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: 23511.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma
#2: Antibody mAb Fab L fragment


Mass: 23893.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma
#3: Chemical ChemComp-XPG / 7-[(1R,3R)-3-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-5-oxocyclopentyl]heptanoic acid / Prostaglandin E1


Mass: 354.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H34O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 753 / 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: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 293 K / Method: oil-microbatch / pH: 6
Details: 0.1M bis-tris-HCl, 25%(w/v) PEG3350 , 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: 1.7→29.05 Å / Num. obs: 53198 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.084
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 4.7 / Num. unique all: 7665 / % possible all: 99.9

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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: 1.7→26.763 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.895 / SU ML: 0.16 / σ(F): 1.35 / Phase error: 17.27 / Stereochemistry target values: ML / Details: The structure was refined also REFMAC5 and CNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1897 2698 5.08 %RANDOM
Rwork0.1679 ---
obs0.169 53128 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.08 Å2 / Biso mean: 19.3299 Å2 / Biso min: 2.26 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3241 0 25 753 4019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043464
X-RAY DIFFRACTIONf_angle_d0.9764733
X-RAY DIFFRACTIONf_chiral_restr0.064535
X-RAY DIFFRACTIONf_plane_restr0.004606
X-RAY DIFFRACTIONf_dihedral_angle_d11.1631218
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
1.7-1.76080.23662760.202349655241
1.7608-1.83130.21362580.182749695227
1.8313-1.91460.19452560.178150005256
1.9146-2.01550.19522620.176149955257
2.0155-2.14170.19572810.168749865267
2.1417-2.3070.20572380.172250445282
2.307-2.5390.18912810.17350095290
2.539-2.9060.20293040.175450435347
2.906-3.65980.17512620.160651125374
3.6598-26.76660.17042800.152753075587

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