[English] 日本語
Yorodumi
- PDB-9e9m: Ligand Free Putative Ancestral Protein Tyrosine Phosphatase ShufP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9e9m
TitleLigand Free Putative Ancestral Protein Tyrosine Phosphatase ShufPTP - C93-Cyclic Sulfenamide - Intermediate p-loop Conformation
ComponentsShufPTP
KeywordsHYDROLASE / phosphatase / inhibitor / ASR / CSO / Oxidized Cystine / Cyclic Sulfenamide
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsDenson, J.M. / Shen, R. / Hengge, A.C. / Johnson, S.J.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: A Putative Ancestral Protein Tyrosine Phosphatase Probes the Evolutionary Origin of PTP Loop Motions
Authors: Shen, R. / Denson, J.M. / Hengge, A.C. / Johnson, S.J.
History
DepositionNov 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ShufPTP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6213
Polymers17,4291
Non-polymers1922
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.032, 86.032, 32.198
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

-
Components

#1: Protein ShufPTP


Mass: 17429.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 8 mg/mL protein, 0.1 M CAPS, 30% PEG 400 at a 1:1:0.2 protein/well/additive screen. The additive screen contains 0.2 M (NH4)2SO4, 20-30% PEG 4000, and 10-35% glycerol.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 19, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 19702 / % possible obs: 98.2 % / Redundancy: 19.6 % / Biso Wilson estimate: 20.76 Å2 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.014 / Rrim(I) all: 0.063 / Χ2: 1.045 / Net I/σ(I): 23.4 / Num. measured all: 385923
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsRpim(I) allRrim(I) allΧ2% possible all
1.55-1.6116.50.53419080.1330.5511.0695.3
1.61-1.6718.20.38319100.0910.3931.08597
1.67-1.7518.10.26919210.0640.2771.04697.8
1.75-1.8418.50.19919560.0470.2041.05597.4
1.84-1.9519.10.14819590.0340.1521.03498
1.95-2.1200.11619510.0260.1191.03498.7
2.1-2.32210.09119840.020.0931.08398.7
2.32-2.6521.60.07320000.0160.0741.03499.7
2.65-3.3421.70.05520180.0120.0560.96999.8
3.34-5020.80.04220950.0090.0431.067100

-
Processing

Software
NameVersionClassification
PDB_EXTRACTdata extraction
PHENIX1.20.1_4487refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→29.56 Å / SU ML: 0.1642 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4925
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2119 992 5.04 %
Rwork0.1853 18695 -
obs0.1867 19687 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.59 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1207 0 10 129 1346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661255
X-RAY DIFFRACTIONf_angle_d0.98191700
X-RAY DIFFRACTIONf_chiral_restr0.0568185
X-RAY DIFFRACTIONf_plane_restr0.0082216
X-RAY DIFFRACTIONf_dihedral_angle_d8.8501172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.630.31531360.23082596X-RAY DIFFRACTION96.43
1.63-1.730.22461400.19182605X-RAY DIFFRACTION96.89
1.73-1.870.24661410.21152628X-RAY DIFFRACTION97.33
1.87-2.060.2341430.18622649X-RAY DIFFRACTION98.17
2.06-2.350.20661420.18872688X-RAY DIFFRACTION99.16
2.35-2.960.19961430.1922732X-RAY DIFFRACTION99.72
2.97-29.560.20041470.17162797X-RAY DIFFRACTION100

+
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