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- PDB-7e8k: Crystal structure of Proteinaceous RNase P (PRORP) from Planctomy... -

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Basic information

Entry
Database: PDB / ID: 7e8k
TitleCrystal structure of Proteinaceous RNase P (PRORP) from Planctomycetes bacterium GWF2_40_8
ComponentsRNA-free ribonuclease P
KeywordsHYDROLASE / proteinaceous RNase P / PRORP / metallonuclease / tRNA 5' maturation / pre-tRNA processing
Function / homologyRNA-free ribonuclease P / PINc domain ribonuclease / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / PIN-like domain superfamily / ligase activity / metal ion binding / RNA-free ribonuclease P
Function and homology information
Biological speciesPlanctomycetes bacterium GWF2_40_8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLi, Y.Y. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870721 China
CitationJournal: Nat Commun / Year: 2022
Title: Crystal structures and insights into precursor tRNA 5'-end processing by prokaryotic minimal protein-only RNase P.
Authors: Li, Y. / Su, S. / Gao, Y. / Lu, G. / Liu, H. / Chen, X. / Shao, Z. / Zhang, Y. / Shao, Q. / Zhao, X. / Yang, J. / Cao, C. / Lin, J. / Ma, J. / Gan, J.
History
DepositionMar 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-free ribonuclease P
B: RNA-free ribonuclease P
C: RNA-free ribonuclease P
D: RNA-free ribonuclease P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,49820
Polymers95,9614
Non-polymers1,53716
Water6,413356
1
A: RNA-free ribonuclease P
B: RNA-free ribonuclease P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,84511
Polymers47,9802
Non-polymers8659
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-117 kcal/mol
Surface area21060 Å2
MethodPISA
2
C: RNA-free ribonuclease P
D: RNA-free ribonuclease P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6539
Polymers47,9802
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-101 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.932, 99.932, 176.178
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 63 or (resid 64...
21(chain B and ((resid 5 and (name N or name...
31(chain C and (resid 5 through 63 or (resid 64...
41(chain D and ((resid 5 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSTYRTYR(chain A and (resid 5 through 63 or (resid 64...AA5 - 6310 - 68
12GLUGLUGLUGLU(chain A and (resid 5 through 63 or (resid 64...AA6469
13LYSLYSMETMET(chain A and (resid 5 through 63 or (resid 64...AA5 - 20310 - 208
21LYSLYSLYSLYS(chain B and ((resid 5 and (name N or name...BB510
22GLYGLYMETMET(chain B and ((resid 5 and (name N or name...BB-2 - 2033 - 208
23GLYGLYMETMET(chain B and ((resid 5 and (name N or name...BB-2 - 2033 - 208
24GLYGLYMETMET(chain B and ((resid 5 and (name N or name...BB-2 - 2033 - 208
25GLYGLYMETMET(chain B and ((resid 5 and (name N or name...BB-2 - 2033 - 208
31LYSLYSTYRTYR(chain C and (resid 5 through 63 or (resid 64...CC5 - 6310 - 68
32GLUGLUGLUGLU(chain C and (resid 5 through 63 or (resid 64...CC6469
33LYSLYSMETMET(chain C and (resid 5 through 63 or (resid 64...CC5 - 20310 - 208
34LYSLYSMETMET(chain C and (resid 5 through 63 or (resid 64...CC5 - 20310 - 208
35LYSLYSMETMET(chain C and (resid 5 through 63 or (resid 64...CC5 - 20310 - 208
41LYSLYSLYSLYS(chain D and ((resid 5 and (name N or name...DD510
42GLYGLYMETMET(chain D and ((resid 5 and (name N or name...DD-2 - 2033 - 208
43GLYGLYMETMET(chain D and ((resid 5 and (name N or name...DD-2 - 2033 - 208
44GLYGLYMETMET(chain D and ((resid 5 and (name N or name...DD-2 - 2033 - 208
45GLYGLYMETMET(chain D and ((resid 5 and (name N or name...DD-2 - 2033 - 208

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Components

#1: Protein
RNA-free ribonuclease P / RNA-free RNase P / Protein-only RNase P


Mass: 23990.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planctomycetes bacterium GWF2_40_8 (bacteria)
Gene: A2106_02805 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1G2XP69, ribonuclease P
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 5.29 Å3/Da / Density % sol: 76.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2000mM Ammonium sulfate, 100mM Sodium citrate/Citric acid pH 5.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.249→30 Å / Num. obs: 92631 / % possible obs: 99 % / Redundancy: 7.1 % / Biso Wilson estimate: 27.21 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.033 / Rrim(I) all: 0.098 / Χ2: 0.997 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.333.80.36186880.6510.1880.410.72492.9
2.33-2.425.10.3792890.7820.1730.410.72499.1
2.42-2.535.70.33992740.8790.1490.3720.77999.6
2.53-2.6760.30593650.920.1290.3330.83599.6
2.67-2.836.30.23492620.9660.0950.2530.99399.4
2.83-3.057.60.19993520.9820.0730.2121.1499.8
3.05-3.368.30.15293390.990.0530.1611.27399.9
3.36-3.858.60.11193640.9940.0380.1181.39699.9
3.85-4.849.90.07893610.9980.0250.0821.12699.9
4.84-309.70.05193370.9990.0170.0540.59899.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7E8J

7e8j


Resolution: 2.25→29.363 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 2.22 / Phase error: 21.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2148 4034 5.05 %
Rwork0.1899 75777 -
obs0.1912 79811 85.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.53 Å2 / Biso mean: 42.4974 Å2 / Biso min: 18.19 Å2
Refinement stepCycle: final / Resolution: 2.25→29.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6442 0 80 356 6878
Biso mean--110.29 40.18 -
Num. residues----803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076612
X-RAY DIFFRACTIONf_angle_d1.1318905
X-RAY DIFFRACTIONf_chiral_restr0.0571027
X-RAY DIFFRACTIONf_plane_restr0.0061107
X-RAY DIFFRACTIONf_dihedral_angle_d14.3854499
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3777X-RAY DIFFRACTION17.855TORSIONAL
12B3777X-RAY DIFFRACTION17.855TORSIONAL
13C3777X-RAY DIFFRACTION17.855TORSIONAL
14D3777X-RAY DIFFRACTION17.855TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.25-2.27520.2975600.255792730
2.2752-2.3030.266580.2541102434
2.303-2.33210.3058720.2574118339
2.3321-2.36280.3103780.25140847
2.3628-2.39520.2626890.2521159752
2.3952-2.42940.25521010.2554178959
2.4294-2.46560.27631100.2617209269
2.4656-2.50410.30061290.2513246979
2.5041-2.54510.29061660.2529262087
2.5451-2.5890.2881440.2472278692
2.589-2.6360.25081870.2373294196
2.636-2.68670.26891450.2279298398
2.6867-2.74150.2541600.2208303399
2.7415-2.80110.20931770.2067304099
2.8011-2.86620.22041690.2182303299
2.8662-2.93780.25091650.20343098100
2.9378-3.01720.19541600.2033026100
3.0172-3.10580.22921220.20593076100
3.1058-3.2060.26151660.20973083100
3.206-3.32040.22481350.19713080100
3.3204-3.45320.21191450.18133081100
3.4532-3.61010.20881650.17693054100
3.6101-3.80.18971580.16283029100
3.8-4.03750.19331620.15973068100
4.0375-4.34840.16791710.14863075100
4.3484-4.78430.16421600.13893041100
4.7843-5.47270.19951620.15493062100
5.4727-6.88030.21331750.20063031100
6.8803-29.3630.15681430.1639304999
Refinement TLS params.Method: refined / Origin x: -1.5118 Å / Origin y: 14.3606 Å / Origin z: 26.3287 Å
111213212223313233
T0.1688 Å20.0025 Å2-0.0094 Å2-0.2934 Å2-0.0121 Å2--0.2251 Å2
L1.3396 °20.0312 °2-0.337 °2--0.0067 °2-0.0115 °2--0.2003 °2
S-0.1666 Å °0.0014 Å °0.0014 Å °0.0088 Å °0.0652 Å °-0.0023 Å °-0.0164 Å °-0.0017 Å °0.0924 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 203
2X-RAY DIFFRACTION1allB-2 - 203
3X-RAY DIFFRACTION1allC5 - 203
4X-RAY DIFFRACTION1allD-2 - 203
5X-RAY DIFFRACTION1allE1 - 15
6X-RAY DIFFRACTION1allE16
7X-RAY DIFFRACTION1allG1 - 553

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