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- PDB-6dsi: Anti recombinant prolactin receptor scFv -

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Basic information

Entry
Database: PDB / ID: 6dsi
TitleAnti recombinant prolactin receptor scFv
ComponentsAnti-TN-C scFv
KeywordsIMMUNE SYSTEM / anti prolactin receptor scFV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 Å
AuthorsLangley, D.B. / Rouet, R. / Christ, D.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1113904 Australia
Australian Research Council (ARC)160104915 Australia
CitationJournal: To Be Published
Title: Anti recombinant prolactin receptor scFv
Authors: Rouet, R. / Langley, D.B. / Christ, D.
History
DepositionJun 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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: Anti-TN-C scFv


Theoretical massNumber of molelcules
Total (without water)25,5601
Polymers25,5601
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Chains A and B are actually the one scFv molecule. They are chained separately to reflect the fact that normally the heavy chain variable domain (chain A) and the light ...Evidence: gel filtration, Chains A and B are actually the one scFv molecule. They are chained separately to reflect the fact that normally the heavy chain variable domain (chain A) and the light chain variable domain (chain B) are normally NOT cojoined, although they embrace each other as expected of an antibody pairing. The bulk of a long linker (16 amino acid residues) is not observed in the electron density. The first five residues of the B-chain belong to this linker.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.280, 133.030, 44.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody Anti-TN-C scFv


Mass: 25560.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.53 Å3/Da / Density % sol: 65.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Equal volumes (2 microlitres) of protein solution (5 mg/mL in 15 mM Tris (pH 7.5) and 50 mM NaCl) were combined with well solution (2% (v/v) Dioxane, 100 mM Bicine (pH 9.0) and 10% (w/v) PEG4000)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.49→37.8 Å / Num. obs: 12684 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.972 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.049 / Rrim(I) all: 0.123 / Net I/σ(I): 10.1
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.513 / Num. unique obs: 1397 / CC1/2: 0.905 / Rpim(I) all: 0.216 / Rrim(I) all: 0.557 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.25 Å36.86 Å
Translation4.25 Å36.86 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.7.1data scaling
PHASER2.8.2phasing
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6dn0

6dn0


Resolution: 2.49→36.86 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.097 / SU ML: 0.175 / SU R Cruickshank DPI: 0.3087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.309 / ESU R Free: 0.236
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 604 4.8 %RANDOM
Rwork0.2069 ---
obs0.2086 12070 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 116.27 Å2 / Biso mean: 43.716 Å2 / Biso min: 23.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20 Å2
2---0.26 Å20 Å2
3---1.67 Å2
Refinement stepCycle: final / Resolution: 2.49→36.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1727 0 0 20 1747
Biso mean---38.8 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0141777
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181506
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.6532409
X-RAY DIFFRACTIONr_angle_other_deg0.9171.6423535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6855229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6012285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.62415270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0361510
X-RAY DIFFRACTIONr_chiral_restr0.070.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02358
LS refinement shellResolution: 2.488→2.552 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 50 -
Rwork0.296 862 -
all-912 -
obs--99.89 %

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