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- PDB-4ozs: RNA binding protein -

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Basic information

Entry
Database: PDB / ID: 4ozs
TitleRNA binding protein
ComponentsAlpha solenoid protein
KeywordsRNA BINDING PROTEIN / RNA / Specificity
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.17 Å
AuthorsGully, B.S. / Bond, C.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The design and structural characterization of a synthetic pentatricopeptide repeat protein.
Authors: Gully, B.S. / Shah, K.R. / Lee, M. / Shearston, K. / Smith, N.M. / Sadowska, A. / Blythe, A.J. / Bernath-Levin, K. / Stanley, W.A. / Small, I.D. / Bond, C.S.
History
DepositionFeb 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.dist / _software.classification
Revision 2.0Aug 22, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / refine_hist / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 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
A: Alpha solenoid protein


Theoretical massNumber of molelcules
Total (without water)19,4811
Polymers19,4811
Non-polymers00
Water81145
1
A: Alpha solenoid protein

A: Alpha solenoid protein

A: Alpha solenoid protein


Theoretical massNumber of molelcules
Total (without water)58,4423
Polymers58,4423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+3/2,-y,z+1/21
crystal symmetry operation2_654-x+3/2,-y,z-1/21
Unit cell
Length a, b, c (Å)54.025, 75.023, 85.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha solenoid protein


Mass: 19480.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1

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Sample preparation

CrystalDensity Matthews: 4.43 Å3/Da / Density % sol: 72.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.35
Details: Diffraction quality crystals grew from 3 uL drops in 24-well sitting drop Cryschem plates (Hampton Research) in 2:1 ratios of crystallant 100 mM Sodium citrate pH 3.35, 8 % (w/v) PEG 3350 ...Details: Diffraction quality crystals grew from 3 uL drops in 24-well sitting drop Cryschem plates (Hampton Research) in 2:1 ratios of crystallant 100 mM Sodium citrate pH 3.35, 8 % (w/v) PEG 3350 and protein equilibrated against 1 mL of crystallant at 293 K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.980, 0.954
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2013
RadiationProtocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.9541
ReflectionResolution: 2.17→56.28 Å / Num. all: 37530 / Num. obs: 18791 / % possible obs: 99.78 % / Redundancy: 2 % / Rmerge(I) obs: 0.01873 / Net I/σ(I): 24.44
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3134 / Mean I/σ(I) obs: 2.68 / % possible all: 98.43

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata scaling
SCALAdata scaling
PHENIXphasing
PHENIXrefinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 2.17→56.28 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.134 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26549 966 5.1 %RANDOM
Rwork0.21691 ---
obs0.21933 17825 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.438 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2---0.99 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 2.17→56.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1365 0 0 45 1410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021386
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4422.0121863
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5395176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.57626.72161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.67915282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.426155
X-RAY DIFFRACTIONr_chiral_restr0.1540.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211004
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.17→2.229 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 59 -
Rwork0.289 1155 -
obs--97.67 %

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