[English] 日本語
Yorodumi
- PDB-1nz0: RNASE P PROTEIN FROM THERMOTOGA MARITIMA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nz0
TitleRNASE P PROTEIN FROM THERMOTOGA MARITIMA
ComponentsRibonuclease P protein component
KeywordsHYDROLASE / ENDONUCLEASE / RNASE / ALFA-BETA SANDWICH / DIMER / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


ribonuclease P complex / 3'-tRNA processing endoribonuclease activity / tRNA 3'-end processing / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / tRNA 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
Ribonuclease P protein component
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å
AuthorsKazantsev, A.V. / Krivenko, A.A. / Harrington, D.J. / Carter, R.J. / Holbrook, S.R. / Adams, P.D. / Pace, N.R. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: High-resolution structure of RNase P protein from Thermotoga maritima.
Authors: Kazantsev, A.V. / Krivenko, A.A. / Harrington, D.J. / Carter, R.J. / Holbrook, S.R. / Adams, P.D. / Pace, N.R.
History
DepositionFeb 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_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 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribonuclease P protein component
C: Ribonuclease P protein component
B: Ribonuclease P protein component
D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,24920
Polymers57,7124
Non-polymers1,53716
Water9,602533
1
A: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6203
Polymers14,4281
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7164
Polymers14,4281
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0047
Polymers14,4281
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9086
Polymers14,4281
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Ribonuclease P protein component
hetero molecules

A: Ribonuclease P protein component
hetero molecules

C: Ribonuclease P protein component
hetero molecules

D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,24920
Polymers57,7124
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_756-x+2,y+1/2,-z+11
crystal symmetry operation2_747-x+2,y-1/2,-z+21
Buried area5710 Å2
ΔGint-205 kcal/mol
Surface area23950 Å2
MethodPISA
6
B: Ribonuclease P protein component
hetero molecules

C: Ribonuclease P protein component
hetero molecules

A: Ribonuclease P protein component
D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,24920
Polymers57,7124
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-207 kcal/mol
Surface area23750 Å2
MethodPISA
7
A: Ribonuclease P protein component
C: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3367
Polymers28,8562
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-74 kcal/mol
Surface area11650 Å2
MethodPISA
8
B: Ribonuclease P protein component
D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,91313
Polymers28,8562
Non-polymers1,05711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-139 kcal/mol
Surface area12430 Å2
MethodPISA
9
B: Ribonuclease P protein component
hetero molecules

D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,91313
Polymers28,8562
Non-polymers1,05711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2680 Å2
ΔGint-133 kcal/mol
Surface area12960 Å2
MethodPISA
10
C: Ribonuclease P protein component
hetero molecules

A: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3367
Polymers28,8562
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area1800 Å2
ΔGint-65 kcal/mol
Surface area12220 Å2
MethodPISA
11
B: Ribonuclease P protein component
hetero molecules

D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,91313
Polymers28,8562
Non-polymers1,05711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_747-x+2,y-1/2,-z+21
Buried area2430 Å2
ΔGint-133 kcal/mol
Surface area13210 Å2
MethodPISA
12
B: Ribonuclease P protein component
hetero molecules

D: Ribonuclease P protein component
hetero molecules

C: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,62917
Polymers43,2843
Non-polymers1,34514
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_756-x+2,y+1/2,-z+11
Buried area4600 Å2
ΔGint-176 kcal/mol
Surface area17990 Å2
MethodPISA
13
B: Ribonuclease P protein component
hetero molecules

C: Ribonuclease P protein component
hetero molecules

D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,62917
Polymers43,2843
Non-polymers1,34514
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y+1/2,-z+11
crystal symmetry operation2_747-x+2,y-1/2,-z+21
Buried area3970 Å2
ΔGint-173 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.227, 64.143, 68.326
Angle α, β, γ (deg.)90.00, 102.02, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 14427.935 Da / Num. of mol.: 4 / Mutation: M1S, L41M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: RNPA OR TM1463 / Plasmid: PGEX4TA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: Q9X1H4, ribonuclease P
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 1500, potassium sulfate, sodium acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion / PH range low: 5.2 / PH range high: 4.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mM1reservoirpH4.8-5.2NaOAc
212-18 %PEG15001reservoir
3200 mM1reservoirK2SO4
43 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9792 / Wavelength: 0.9792 Å
DetectorType: ADSC / Detector: CCD / Date: May 11, 2001 / Details: W16 WIGGLER
RadiationMonochromator: DOUBLE-CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. all: 118678 / Num. obs: 118678 / % possible obs: 80 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 6.53 % / Biso Wilson estimate: 13.688 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 5.3
Reflection shellResolution: 1.2→1.35 Å / Redundancy: 4.01 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 1.1 / Num. unique all: 16982 / Rsym value: 0.565 / % possible all: 38.7
Reflection
*PLUS
Num. measured all: 774818
Reflection shell
*PLUS
% possible obs: 38.7 % / Num. unique obs: 16982 / Num. measured obs: 67203

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXmodel building
SHELXL-97refinement
CCP4(SCALA)data scaling
CNSphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.2→30 Å / Num. parameters: 41196 / Num. restraintsaints: 57603 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.14%
RfactorNum. reflection% reflectionSelection details
Rfree0.217 5799 4.9 %RANDOM
Rwork0.1625 ---
all0.1634 118678 --
obs0.1625 117875 79.6 %-
Refine analyzeNum. disordered residues: 148 / Occupancy sum hydrogen: 3913 / Occupancy sum non hydrogen: 4230.3
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 0 80 533 4577
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0.009
X-RAY DIFFRACTIONs_from_restr_planes0.0287
X-RAY DIFFRACTIONs_zero_chiral_vol0.134
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.141
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.043
X-RAY DIFFRACTIONs_approx_iso_adps0.076
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rwork: 0.1634
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.715
X-RAY DIFFRACTIONs_plane_restr0.029
X-RAY DIFFRACTIONs_chiral_restr0.134

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more