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- PDB-4rou: Auto-inhibition Mechanism of Human Mitochondrial RNase P Protein ... -

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Basic information

Entry
Database: PDB / ID: 4rou
TitleAuto-inhibition Mechanism of Human Mitochondrial RNase P Protein Complex
ComponentsMitochondrial ribonuclease P protein 3
KeywordsHYDROLASE / mitochondria
Function / homology
Function and homology information


rRNA processing in the mitochondrion / tRNA processing in the mitochondrion / tRNA modification in the mitochondrion / mitochondrial ribonuclease P complex / mitochondrial tRNA 5'-end processing / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / mitochondrial nucleoid / mitochondrial matrix ...rRNA processing in the mitochondrion / tRNA processing in the mitochondrion / tRNA modification in the mitochondrion / mitochondrial ribonuclease P complex / mitochondrial tRNA 5'-end processing / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / mitochondrial nucleoid / mitochondrial matrix / mitochondrion / nucleoplasm / metal ion binding
Similarity search - Function
Mitochondrial ribonuclease P catalytic subunit / Protein-only RNase P, C-terminal / Protein-only RNase P / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Mitochondrial ribonuclease P catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.713 Å
AuthorsLi, F. / Liu, X. / Yang, X. / Shen, Y.
CitationJournal: TO BE PUBLISHED
Title: Auto-inhibition Mechanism of Human Mitochondrial RNase P Protein Complex
Authors: Li, F. / Liu, X. / Yang, X. / Shen, Y.
History
DepositionOct 29, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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

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Assembly

Deposited unit
B: Mitochondrial ribonuclease P protein 3
A: Mitochondrial ribonuclease P protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4867
Polymers72,2492
Non-polymers2375
Water1629
1
B: Mitochondrial ribonuclease P protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2253
Polymers36,1241
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Mitochondrial ribonuclease P protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2614
Polymers36,1241
Non-polymers1363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-22 kcal/mol
Surface area24060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.434, 78.287, 114.187
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 Mitochondrial ribonuclease P protein 3 / Mitochondrial RNase P protein 3


Mass: 36124.348 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15091
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M MgCl2, 0.1M HEPES pH 7.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 25, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.713→50 Å / Num. all: 18642 / Num. obs: 16469 / % possible obs: 88.34 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 7.1 %
Reflection shellHighest resolution: 2.713 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.713→46.129 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 31.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 812 4.93 %RANDOM
Rwork0.2385 ---
obs0.2405 16469 98.64 %-
all-18642 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.713→46.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3884 0 5 9 3898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053975
X-RAY DIFFRACTIONf_angle_d0.9375382
X-RAY DIFFRACTIONf_dihedral_angle_d14.0891372
X-RAY DIFFRACTIONf_chiral_restr0.044603
X-RAY DIFFRACTIONf_plane_restr0.005679
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7135-2.88350.35691290.2879255498
2.8835-3.10610.30331190.28652603100
3.1061-3.41860.34651350.26342619100
3.4186-3.9130.26971510.22942625100
3.913-4.92910.24441320.20142649100
4.9291-46.1360.26571460.2476260794
Refinement TLS params.Method: refined / Origin x: -5.3955 Å / Origin y: 0.5977 Å / Origin z: -3.7382 Å
111213212223313233
T0.3924 Å20.1117 Å2-0.0126 Å2-0.1809 Å2-0.0241 Å2--0.3532 Å2
L2.0944 °20.5107 °2-0.9706 °2-0.8081 °2-0.3626 °2--2.5632 °2
S-0.0638 Å °0.0263 Å °-0.1126 Å °-0.0143 Å °-0.038 Å °-0.0328 Å °0.0128 Å °-0.1276 Å °0.1081 Å °
Refinement TLS groupSelection details: all

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