[English] 日本語
Yorodumi
- PDB-4nyh: Orthorhombic crystal form of pir1 dual specificity phosphatase core -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nyh
TitleOrthorhombic crystal form of pir1 dual specificity phosphatase core
ComponentsRNA/RNP complex-1-interacting phosphatase
KeywordsHYDROLASE / Dual Specificity Phosphatase / Protein tyrosine Phosphatase / P-loop / Protein Tyrosine Phosphatase (PTP)-fold / RNA-RNP COMPLEX-1 / Dephosphorylation / NUCLEUS
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / polynucleotide 5'-phosphatase activity / intercellular bridge / phosphatase activity / RNA processing / protein dephosphorylation / protein tyrosine phosphatase activity / fibrillar center / nuclear speck / RNA binding ...Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / polynucleotide 5'-phosphatase activity / intercellular bridge / phosphatase activity / RNA processing / protein dephosphorylation / protein tyrosine phosphatase activity / fibrillar center / nuclear speck / RNA binding / nucleoplasm / nucleus
Similarity search - Function
: / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site ...: / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / RNA/RNP complex-1-interacting phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSankhala, R.S. / Lokareddy, R.K. / Cingolani, G.
CitationJournal: Biochemistry / Year: 2014
Title: Structure of Human PIR1, an Atypical Dual-Specificity Phosphatase.
Authors: Sankhala, R.S. / Lokareddy, R.K. / Cingolani, G.
History
DepositionDec 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / 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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA/RNP complex-1-interacting phosphatase
B: RNA/RNP complex-1-interacting phosphatase
C: RNA/RNP complex-1-interacting phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0949
Polymers63,7033
Non-polymers3916
Water14,970831
1
A: RNA/RNP complex-1-interacting phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3653
Polymers21,2341
Non-polymers1302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA/RNP complex-1-interacting phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3653
Polymers21,2341
Non-polymers1302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA/RNP complex-1-interacting phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3653
Polymers21,2341
Non-polymers1302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.026, 62.723, 178.773
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYARGARGAA24 - 2051 - 182
21GLYGLYARGARGBB24 - 2051 - 182
12ASNASNILEILEAA29 - 2046 - 181
22ASNASNILEILECC29 - 2046 - 181
13ASNASNILEILEBB29 - 2046 - 181
23ASNASNILEILECC29 - 2046 - 181

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein RNA/RNP complex-1-interacting phosphatase / Dual specificity protein phosphatase 11 / Phosphatase that interacts with RNA/RNP complex 1


Mass: 21234.215 Da / Num. of mol.: 3 / Fragment: UNP residues 29-205 / Mutation: C152S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP11, PIR1 / Production host: Escherichia coli (E. coli)
References: UniProt: O75319, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#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.: 831 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M Potassium thiocyanate, 30% w/v Polyethylene glycol monomethyl ether 2,000, pH 5.5, VAPOR DIFFUSION, temperature 290K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.07
SYNCHROTRONNSLS X6A20.972
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMar 19, 2013
ADSC QUANTUM 2702CCDApr 19, 2013
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.071
20.9721
ReflectionResolution: 1.2→15 Å / Num. all: 163044 / Num. obs: 163044 / % possible obs: 91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.2-1.243.030.482155.2
1.24-1.294.420.393174.9
1.29-1.357.280.323195.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→6 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.477 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 1.059 / ESU R: 0.039 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16992 8102 5 %RANDOM
Rwork0.13732 ---
all0.1411 163044 --
obs0.13897 153934 90.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.804 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å2-0 Å20 Å2
2---1.02 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4462 0 18 831 5311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194598
X-RAY DIFFRACTIONr_bond_other_d0.0030.024448
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9746222
X-RAY DIFFRACTIONr_angle_other_deg0.8783.00210167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7345540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.07123.934244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25515811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.251536
X-RAY DIFFRACTIONr_chiral_restr0.0890.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0215168
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021088
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3531.9132163
X-RAY DIFFRACTIONr_mcbond_other4.3531.9132162
X-RAY DIFFRACTIONr_mcangle_it4.8542.8782699
X-RAY DIFFRACTIONr_mcangle_other4.8542.8782700
X-RAY DIFFRACTIONr_scbond_it5.8722.3532435
X-RAY DIFFRACTIONr_scbond_other5.872.3552432
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5983.3663517
X-RAY DIFFRACTIONr_long_range_B_refined6.96218.826192
X-RAY DIFFRACTIONr_long_range_B_other6.50617.2455655
X-RAY DIFFRACTIONr_rigid_bond_restr6.93839046
X-RAY DIFFRACTIONr_sphericity_free32.0515214
X-RAY DIFFRACTIONr_sphericity_bonded18.24859554
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A118230.13
12B118230.13
21A115400.12
22C115400.12
31B115790.12
32C115790.12
LS refinement shellResolution: 1.201→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 368 -
Rwork0.32 6192 -
obs--51.91 %

+
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