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- PDB-4jg4: Ligand concentration regulates the pathways of coupled protein fo... -

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Basic information

Entry
Database: PDB / ID: 4jg4
TitleLigand concentration regulates the pathways of coupled protein folding and binding
ComponentsRibonuclease P protein component
KeywordsHYDROLASE / RNA-Binding / Endonuclease
Function / homology
Function and homology information


anion binding / 3'-tRNA processing endoribonuclease activity / ribonuclease P RNA binding / ribonuclease P complex / tRNA 3'-end processing / ribonuclease P / sulfate binding / ribonuclease P activity / tRNA 5'-leader removal / chloride ion binding ...anion binding / 3'-tRNA processing endoribonuclease activity / ribonuclease P RNA binding / ribonuclease P complex / tRNA 3'-end processing / ribonuclease P / sulfate binding / ribonuclease P activity / tRNA 5'-leader removal / chloride ion binding / phosphate ion binding / tRNA binding / molecular adaptor activity / DNA binding
Similarity search - Function
Ribonuclease P / Ribonuclease P, conserved site / Ribonuclease P / Bacterial ribonuclease P protein component signature. / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE / Ribonuclease P protein component / Ribonuclease P protein component
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.296 Å
AuthorsTonthat, N.K.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Ligand concentration regulates the pathways of coupled protein folding and binding.
Authors: Daniels, K.G. / Tonthat, N.K. / McClure, D.R. / Chang, Y.C. / Liu, X. / Schumacher, M.A. / Fierke, C.A. / Schmidler, S.C. / Oas, T.G.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6754
Polymers14,1421
Non-polymers5343
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.152, 83.152, 32.236
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

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Components

#1: Protein Ribonuclease P protein component / RNase P protein / RNaseP protein / Protein C5


Mass: 14141.511 Da / Num. of mol.: 1 / Mutation: F107W, P39A, P90A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: rnpA, BSSC8_00790 / Production host: Escherichia coli (E. coli)
References: UniProt: G4ENZ9, UniProt: P25814*PLUS, ribonuclease P
#2: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4O7P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.16 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→24.02 Å / Num. obs: 5545 / % possible obs: 94.4 % / Redundancy: 8.9 % / Rsym value: 0.048 / Net I/σ(I): 44.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 11.9 / Rsym value: 0.126 / % possible all: 78.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1111)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementResolution: 2.296→24.017 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.31 / σ(F): 1.45 / Phase error: 25.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 554 10.01 %
Rwork0.2126 --
obs0.2161 5536 94.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.6768 Å2
Refinement stepCycle: LAST / Resolution: 2.296→24.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 27 32 1013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01990
X-RAY DIFFRACTIONf_angle_d1.4881323
X-RAY DIFFRACTIONf_dihedral_angle_d26.219394
X-RAY DIFFRACTIONf_chiral_restr0.095140
X-RAY DIFFRACTIONf_plane_restr0.004160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2962-2.52710.32161240.28291077X-RAY DIFFRACTION84
2.5271-2.89220.31931410.26481258X-RAY DIFFRACTION96
2.8922-3.64180.27581450.22271309X-RAY DIFFRACTION100
3.6418-24.01820.19681440.17691338X-RAY DIFFRACTION99
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)
10.5209-0.1117-0.01730.29150.13370.0245-0.1994-0.03090.0467-0.20260.09850.1087-0.0817-0.2552-0.00010.36020.0315-0.09860.3606-0.06890.307854.1483-149.1558-4.5254
20.1121-0.1225-0.20320.14750.03820.8455-0.01550.05770.13250.0904-0.10780.13050.49840.2049-0.24840.18460.00880.00970.2248-0.02430.34348.1245-151.5996-3.8661
30.05210.04210.05890.03530.04820.07130.19030.0070.0533-0.04710.19180.03620.1115-0.10570.20090.4338-0.2935-0.00251.1080.0840.733772.0587-150.2935-11.0768
40.4022-0.07860.37810.1290.0250.37220.117-0.0475-0.5948-0.0363-0.16410.0354-0.34290.1926-0.0230.1770.01050.05880.1759-0.03210.230657.8146-159.3833-3.5792
50.6376-0.4084-0.18121.44560.44510.173-0.3547-0.78530.19590.40790.4273-0.27650.0327-0.11270.08640.23660.07820.00070.42-0.00160.188160.511-155.69223.5153
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 50 )
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 56 )
4X-RAY DIFFRACTION4chain 'A' and (resid 57 through 81 )
5X-RAY DIFFRACTION5chain 'A' and (resid 82 through 115 )

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