[English] 日本語
Yorodumi
- PDB-7r66: Structure of Pfp1 protease from Thermococcus thioreducens: large ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7r66
TitleStructure of Pfp1 protease from Thermococcus thioreducens: large unit cell at 1.44 A resolution
ComponentsPeptidaseProtease
KeywordsHYDROLASE / intracellular / disulfide bonds / catalytic triad / proteasome / bacteria / supersite
Function / homologyDeglycase PfpI / PfpI endopeptidase domain profile. / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase-like / PHOSPHATE ION / Peptidase
Function and homology information
Biological speciesThermococcus thioreducens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsMcPherson, A.
CitationJournal: Acta Crystallogr. / Year: 2017
Title: Structure of the Pfp1 protease from a hypothermophilic archer, Thermococcus thioreducens, in two crystal forms
Authors: Larson, S.B. / McPherson, A.
History
DepositionJun 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidase
B: Peptidase
C: Peptidase
D: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,50710
Polymers73,8444
Non-polymers6636
Water10,773598
1
A: Peptidase
B: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2775
Polymers36,9222
Non-polymers3553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-29 kcal/mol
Surface area12810 Å2
MethodPISA
2
C: Peptidase
D: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2305
Polymers36,9222
Non-polymers3083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-38 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.030, 151.030, 80.716
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

-
Components

#1: Protein
Peptidase / Protease / intracellular protease


Mass: 18461.092 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus thioreducens (archaea) / Gene: AMR53_10535 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Q2XKL6
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50 % / Description: hexagonal prisms
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sitting drop crystallization using Cryschem plates. Drops were equal amounts of a 25 mg / ml protein stock solution in water and the reservoir solution. The reservoir was 1.4 M sodium ...Details: Sitting drop crystallization using Cryschem plates. Drops were equal amounts of a 25 mg / ml protein stock solution in water and the reservoir solution. The reservoir was 1.4 M sodium citrate at pH 6.5. Crystallization was at room temperature. Drops were 10 ul total starting volume, reservoirs 0.6 ml.
PH range: 6.0 - 7.0

-
Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS EIGER X 500K / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.38→75 Å / Num. obs: 141230 / % possible obs: 100 % / Redundancy: 47 % / Biso Wilson estimate: 19.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.44 / Rrim(I) all: 0.221 / Rsym value: 0.21 / Net I/σ(I): 11.9
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 19.8 % / Mean I/σ(I) obs: 0.3 / Num. unique obs: 7080 / CC1/2: 0.073 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TXW

5txw


Resolution: 1.44→68.69 Å / SU ML: 0.1423 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.5948
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1659 6116 4.92 %
Rwork0.1339 118119 -
obs0.1355 124235 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.88 Å2
Refinement stepCycle: LAST / Resolution: 1.44→68.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 42 598 5836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01065555
X-RAY DIFFRACTIONf_angle_d1.17367559
X-RAY DIFFRACTIONf_chiral_restr0.0824848
X-RAY DIFFRACTIONf_plane_restr0.0142967
X-RAY DIFFRACTIONf_dihedral_angle_d13.64342111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.460.30682060.29223928X-RAY DIFFRACTION99.95
1.46-1.470.29222300.27033937X-RAY DIFFRACTION99.95
1.47-1.490.32181900.2673970X-RAY DIFFRACTION100
1.49-1.510.31112440.24413880X-RAY DIFFRACTION100
1.51-1.530.27271890.22543930X-RAY DIFFRACTION99.95
1.53-1.550.25182000.2083954X-RAY DIFFRACTION99.98
1.55-1.570.25581970.19024018X-RAY DIFFRACTION100
1.57-1.60.23241840.17243846X-RAY DIFFRACTION100
1.6-1.620.18182040.14893988X-RAY DIFFRACTION99.98
1.62-1.650.17552250.1423903X-RAY DIFFRACTION100
1.65-1.680.20031900.143948X-RAY DIFFRACTION99.93
1.68-1.710.18161830.13043966X-RAY DIFFRACTION100
1.71-1.740.18251960.12353936X-RAY DIFFRACTION100
1.74-1.780.16992000.11793940X-RAY DIFFRACTION100
1.78-1.810.16482060.10923920X-RAY DIFFRACTION100
1.81-1.860.15992460.11513951X-RAY DIFFRACTION100
1.86-1.90.17722040.11663920X-RAY DIFFRACTION99.9
1.9-1.950.19382000.13883930X-RAY DIFFRACTION99.85
1.95-2.010.15872000.10813946X-RAY DIFFRACTION100
2.01-2.080.13842370.10523908X-RAY DIFFRACTION100
2.08-2.150.13542010.10543917X-RAY DIFFRACTION100
2.15-2.240.1421910.10953955X-RAY DIFFRACTION99.66
2.24-2.340.16552160.11243915X-RAY DIFFRACTION99.69
2.34-2.460.13481770.11523958X-RAY DIFFRACTION100
2.46-2.620.15292110.11383943X-RAY DIFFRACTION100
2.62-2.820.14672070.11893913X-RAY DIFFRACTION99.98
2.82-3.10.17812050.13683966X-RAY DIFFRACTION100
3.1-3.550.15082100.12743922X-RAY DIFFRACTION100
3.55-4.470.14091930.12013943X-RAY DIFFRACTION99.98
4.47-68.690.17291740.16533968X-RAY DIFFRACTION99.83

+
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