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- PDB-2r8s: High resolution structure of a specific synthetic FAB bound to P4... -

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Basic information

Entry
Database: PDB / ID: 2r8s
TitleHigh resolution structure of a specific synthetic FAB bound to P4-P6 RNA ribozyme domain
Components
  • Fab heavy chain
  • Fab light chain
  • P4-P6 RNA RIBOZYME DOMAIN
KeywordsIMMUNE SYSTEM/RNA / protein-RNA complex / Fab-RNA complex / IMMUNE SYSTEM-RNA COMPLEX
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsYe, J.D. / Tereshko, V. / Sidhu, S.S. / Koide, S. / Kossiakoff, A.A. / Piccirilli, J.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Synthetic antibodies for specific recognition and crystallization of structured RNA
Authors: Ye, J.D. / Tereshko, V. / Frederiksen, J.K. / Koide, A. / Fellouse, F.A. / Sidhu, S.S. / Koide, S. / Kossiakoff, A.A. / Piccirilli, J.A.
History
DepositionSep 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 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
R: P4-P6 RNA RIBOZYME DOMAIN
L: Fab light chain
H: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4557
Polymers98,3583
Non-polymers974
Water9,530529
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-92 kcal/mol
Surface area41880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.085, 53.230, 160.555
Angle α, β, γ (deg.)90.00, 108.42, 90.00
Int Tables number5
Space group name H-MC121
DetailsThis entry contain one asymmetric unit composed of Fab light and heavy chains L and H and RNA chain R.

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Components

#1: RNA chain P4-P6 RNA RIBOZYME DOMAIN


Mass: 51420.559 Da / Num. of mol.: 1 / Mutation: Delta C209 / Source method: obtained synthetically
Details: sequence occurs naturally in Tetrahymena thermophila; synthesized by in vitro transcription
References: GenBank: 10840
#2: Antibody Fab light chain


Mass: 23273.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: FAB SELECTION WAS DONE USING A REDUCED CODON FAB LIBRARY DISPLAYED ON THE M13 PHAGE
Source: (natural) Mus musculus (house mouse)
#3: Antibody Fab heavy chain


Mass: 23663.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: FAB SELECTION WAS DONE USING A REDUCED CODON FAB LIBRARY DISPLAYED ON THE M13 PHAGE
Source: (natural) Mus musculus (house mouse)
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 34% MPD, 0.1M sodium citrate, 0.2M ammonium acetate, 25 mM magnesium chloride, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium citrate11
3ammonium acetate11
4MgCl211
5MPD12
6sodium citrate12
7ammonium acetate12
8MgCl212

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
1,2,31
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 19-BM1
SYNCHROTRONAPS 23-ID-D2
SYNCHROTRONAPS 22-ID3
Detector
TypeIDDetectorDateDetails
SBC-21CCDMay 29, 2006mirrors
MAR scanner 345 mm plate2IMAGE PLATEJun 5, 2006mirrors
MAR scanner 345 mm plate3IMAGE PLATEJun 15, 2006mirrors
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 77127 / Num. obs: 77127 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.7
Reflection shellResolution: 1.95→2 Å / % possible obs: 95.5 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TZI 1HR2

1tzi

1hr2


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.147 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.157 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22607 3875 5 %RANDOM
Rwork0.19476 ---
all0.19632 77127 --
obs0.19632 77127 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.918 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å20 Å2-0.4 Å2
2--0.94 Å20 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3263 3404 4 529 7200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.027180
X-RAY DIFFRACTIONr_bond_other_d0.0020.023546
X-RAY DIFFRACTIONr_angle_refined_deg1.332.51710516
X-RAY DIFFRACTIONr_angle_other_deg1.0222.488877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4455429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95424.016127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12415531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9911513
X-RAY DIFFRACTIONr_chiral_restr0.0590.21310
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025403
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02670
X-RAY DIFFRACTIONr_nbd_refined0.1620.21167
X-RAY DIFFRACTIONr_nbd_other0.2050.24062
X-RAY DIFFRACTIONr_nbtor_refined0.2120.23089
X-RAY DIFFRACTIONr_nbtor_other0.080.22451
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2605
X-RAY DIFFRACTIONr_metal_ion_refined0.0380.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.231
X-RAY DIFFRACTIONr_mcbond_it1.2711.52182
X-RAY DIFFRACTIONr_mcbond_other0.3261.5873
X-RAY DIFFRACTIONr_mcangle_it2.09223482
X-RAY DIFFRACTIONr_scbond_it2.34936768
X-RAY DIFFRACTIONr_scangle_it3.1834.57034
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 261 -
Rwork0.253 5207 -
obs--96.12 %
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)
10.3487-0.044-0.17340.18810.09850.5512-0.07580.15970.0044-0.07140.05290.03450.10540.02360.02290.01970.0260.00570.01760.0039-0.048673.6258-30.995720.2968
20.8963-0.4232-0.21120.82090.25210.30820.0560.04670.0469-0.0504-0.09830.0109-0.03-0.10650.0423-0.03210.068-0.0331-0.0397-0.0041-0.056737.48171.89146.7597
30.9529-0.2678-0.41820.55930.21670.67220.0628-0.0518-0.03150.009-0.0877-0.05080.0046-0.06160.0249-0.01120.0194-0.0112-0.05120.0046-0.050151.3201-1.654858.6821
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1R102 - 261
2X-RAY DIFFRACTION1R1001 - 1004
3X-RAY DIFFRACTION2L1 - 214
4X-RAY DIFFRACTION2L1001 - 1131
5X-RAY DIFFRACTION3H1 - 224
6X-RAY DIFFRACTION3H1001 - 1141

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