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- PDB-6f7t: Crystal Structure of an Fab fragment in complex with a peptide fr... -

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Basic information

Entry
Database: PDB / ID: 6f7t
TitleCrystal Structure of an Fab fragment in complex with a peptide from Bacillus subtilis RNase Y
Components
  • FAB RY79-90, HEAVY CHAIN
  • FAB RY79-90, LIGHT CHAIN
  • Ribonuclease Y
KeywordsIMMUNE SYSTEM / Fab-peptide complex / lambda x light chain / RNase Y
Function / homology
Function and homology information


mRNA catabolic process / RNA endonuclease activity / mRNA processing / Hydrolases; Acting on ester bonds / membrane => GO:0016020 / RNA binding / identical protein binding / plasma membrane
Similarity search - Function
Ribonuclease Y / Ribonuclease Y, N-terminal / RNase Y N-terminal region / HDIG domain / KH domain / HD domain profile. / K Homology domain, type 1 / HD domain / HD domain / Type-1 KH domain profile. ...Ribonuclease Y / Ribonuclease Y, N-terminal / RNase Y N-terminal region / HDIG domain / KH domain / HD domain profile. / K Homology domain, type 1 / HD domain / HD domain / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / K Homology domain / K homology RNA-binding domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Bacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGolinelli-Pimpaneau, B. / Hardouin, P.
Funding support France, 2items
OrganizationGrant numberCountry
LABEX DynamoANR-11-LABX-0011 France
French National Research AgencyANR-11-BSV8-026 France
CitationJournal: Biophys. J. / Year: 2018
Title: Dissociation of the Dimer of the Intrinsically Disordered Domain of RNase Y upon Antibody Binding.
Authors: Hardouin, P. / Velours, C. / Bou-Nader, C. / Assrir, N. / Laalami, S. / Putzer, H. / Durand, D. / Golinelli-Pimpaneau, B.
History
DepositionDec 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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: FAB RY79-90, LIGHT CHAIN
B: FAB RY79-90, HEAVY CHAIN
C: Ribonuclease Y
D: Ribonuclease Y
H: FAB RY79-90, HEAVY CHAIN
L: FAB RY79-90, LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0977
Polymers96,0736
Non-polymers241
Water4,648258
1
A: FAB RY79-90, LIGHT CHAIN
B: FAB RY79-90, HEAVY CHAIN
D: Ribonuclease Y


Theoretical massNumber of molelcules
Total (without water)48,0373
Polymers48,0373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-28 kcal/mol
Surface area20630 Å2
MethodPISA
2
C: Ribonuclease Y
H: FAB RY79-90, HEAVY CHAIN
L: FAB RY79-90, LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0614
Polymers48,0373
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-27 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.680, 130.450, 72.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11L-301-

MG

21L-430-

HOH

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Components

#1: Antibody FAB RY79-90, LIGHT CHAIN


Mass: 23633.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody FAB RY79-90, HEAVY CHAIN


Mass: 22799.588 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide Ribonuclease Y / RNase Y


Mass: 1603.739 Da / Num. of mol.: 2 / Fragment: UNP residues 79-90 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria)
References: UniProt: O31774, Hydrolases; Acting on ester bonds
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2M MgCl2; 0.1M TRIS; 16% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 29393 / % possible obs: 99.7 % / Redundancy: 8.7 % / Biso Wilson estimate: 84.31 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.6
Reflection shellResolution: 2.6→2.75 Å / Redundancy: 8.63 % / Mean I/σ(I) obs: 1.41 / CC1/2: 0.586 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDS0.7.14data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QHR

2qhr


Resolution: 2.6→46.15 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 1.249 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.905 / SU Rfree Blow DPI: 0.321 / SU Rfree Cruickshank DPI: 0.321
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1464 5 %RANDOM
Rwork0.202 ---
obs0.204 29299 100 %-
Displacement parametersBiso mean: 84.68 Å2
Baniso -1Baniso -2Baniso -3
1--2.8445 Å20 Å20 Å2
2---4.3245 Å20 Å2
3---7.169 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.6→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6741 0 1 258 7000
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016929HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.269441HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2303SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1153HARMONIC5
X-RAY DIFFRACTIONt_it6929HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion21.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion942SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7606SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.69 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2881 141 4.99 %
Rwork0.2261 2684 -
all0.2292 2825 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.35910.0260.21260.6595-0.12290.77530.08110.034-0.08-0.0017-0.0137-0.03490.0189-0.2937-0.0674-0.22690.0420.0067-0.00010.0083-0.2262-17.3109-2.8843-43.5537
20.33390.14880.42480.6565-0.41660.17490.021-0.1295-0.0688-0.07530.05520.21750.0064-0.3305-0.0763-0.18760.0459-0.01970.08440.0197-0.0647-32.5924-1.4173-45.327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* L|* C|*}
2X-RAY DIFFRACTION2{ B|* H|* D|*}

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