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- PDB-6lfx: Crystal structure of PCB4scFv(hN56D) in complex with PCB#77 -

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Basic information

Entry
Database: PDB / ID: 6lfx
TitleCrystal structure of PCB4scFv(hN56D) in complex with PCB#77
ComponentsPCB4scFv(hN56D)
KeywordsIMMUNE SYSTEM / Co-PCB / antibody fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-OM4
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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#77
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
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

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Assembly

Deposited unit
A: PCB4scFv(hN56D)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5252
Polymers27,2371
Non-polymers2881
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11030 Å2
Unit cell
Length a, b, c (Å)91.842, 91.842, 53.969
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-OM4 / 1,2-bis(chloranyl)-4-(3-chloranyl-4-methoxy-phenyl)benzene


Mass: 287.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9Cl3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: CHES, 30% PEG 3350

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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: Nov 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→32.68 Å / Num. obs: 41553 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.78 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 40.4
Reflection shellResolution: 1.43→1.45 Å / Rmerge(I) obs: 0.457 / Num. unique obs: 2078

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ESU

3esu


Resolution: 1.43→32.68 Å / SU ML: 0.1213 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 14.3545
RfactorNum. reflection% reflection
Rfree0.1656 2102 5.06 %
Rwork0.1355 --
obs0.137 41552 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.78 Å2
Refinement stepCycle: LAST / Resolution: 1.43→32.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 17 238 2089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912055
X-RAY DIFFRACTIONf_angle_d1.12412818
X-RAY DIFFRACTIONf_chiral_restr0.1058308
X-RAY DIFFRACTIONf_plane_restr0.0065361
X-RAY DIFFRACTIONf_dihedral_angle_d13.2072781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.460.18941510.15762609X-RAY DIFFRACTION99.32
1.46-1.50.18921640.13692591X-RAY DIFFRACTION100
1.5-1.540.17631360.12832615X-RAY DIFFRACTION100
1.54-1.590.16251540.12742605X-RAY DIFFRACTION100
1.59-1.640.16851240.12382653X-RAY DIFFRACTION100
1.64-1.70.20171550.1262575X-RAY DIFFRACTION100
1.7-1.760.16181690.12722579X-RAY DIFFRACTION100
1.76-1.840.15511000.11992671X-RAY DIFFRACTION100
1.84-1.940.16251380.1172622X-RAY DIFFRACTION100
1.94-2.060.14831100.11992649X-RAY DIFFRACTION100
2.06-2.220.15191500.12312615X-RAY DIFFRACTION100
2.22-2.450.15171660.12962629X-RAY DIFFRACTION100
2.45-2.80.15311260.13642651X-RAY DIFFRACTION100
2.8-3.530.15051240.142673X-RAY DIFFRACTION100
3.53-32.680.19051350.15332713X-RAY DIFFRACTION99.93

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