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- PDB-6lfw: Crystal structure of PCB4scFv(hN56D) in complex with PCB#126 -

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Basic information

Entry
Database: PDB / ID: 6lfw
TitleCrystal structure of PCB4scFv(hN56D) in complex with PCB#126
ComponentsPCB4scFv(hN56D)
KeywordsIMMUNE SYSTEM / Co-PCB / antibody fragment
Function / homologyChem-OMF
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsNakamura, T. / Yamagata, Y. / Morioka, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: To Be Published
Title: Crystal structure of PCB4scFv(hN56D) in complex with PCB#126
Authors: Nakamura, T. / Morioka, H.
History
DepositionDec 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PCB4scFv(hN56D)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5823
Polymers27,2371
Non-polymers3452
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-6 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.210, 92.210, 51.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Antibody PCB4scFv(hN56D)


Mass: 27237.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-OMF / 1,2,3-tris(chloranyl)-5-(3-chloranyl-4-methoxy-phenyl)benzene


Mass: 322.014 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H8Cl4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: CHES, 30% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.41→32.6 Å / Num. obs: 41510 / % possible obs: 99.3 % / Redundancy: 12.9 % / Biso Wilson estimate: 12.62 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 26.4
Reflection shellResolution: 1.41→1.45 Å / Rmerge(I) obs: 0.318 / Num. unique obs: 2792

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ESU

3esu


Resolution: 1.41→32.6 Å / SU ML: 0.1084 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 13.9735
RfactorNum. reflection% reflection
Rfree0.1555 2095 5.05 %
Rwork0.126 --
obs0.1275 41507 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.58 Å2
Refinement stepCycle: LAST / Resolution: 1.41→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 19 310 2119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682041
X-RAY DIFFRACTIONf_angle_d0.98182804
X-RAY DIFFRACTIONf_chiral_restr0.0922311
X-RAY DIFFRACTIONf_plane_restr0.0055358
X-RAY DIFFRACTIONf_dihedral_angle_d12.88769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.440.18641370.14112368X-RAY DIFFRACTION90.27
1.44-1.480.19361510.12662587X-RAY DIFFRACTION99.93
1.48-1.520.14041480.11172642X-RAY DIFFRACTION100
1.52-1.560.17961210.1112634X-RAY DIFFRACTION100
1.56-1.610.14751300.11082636X-RAY DIFFRACTION100
1.61-1.670.16581220.1142656X-RAY DIFFRACTION100
1.67-1.740.17471310.11472661X-RAY DIFFRACTION100
1.74-1.820.16471460.12192604X-RAY DIFFRACTION100
1.82-1.910.15791440.12182648X-RAY DIFFRACTION100
1.91-2.030.1651280.11932645X-RAY DIFFRACTION100
2.03-2.190.17021590.11992662X-RAY DIFFRACTION100
2.19-2.410.14881290.12882638X-RAY DIFFRACTION100
2.41-2.760.16741720.13692621X-RAY DIFFRACTION99.96
2.76-3.480.14241320.12622692X-RAY DIFFRACTION100
3.48-32.60.13621450.1352718X-RAY DIFFRACTION99.93

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