[English] 日本語
Yorodumi
- PDB-8wzd: The Crystal Structure of PKCi from Biortus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wzd
TitleThe Crystal Structure of PKCi from Biortus
ComponentsAdenosine 5'-monophosphoramidase HINT1
KeywordsHYDROLASE / Histidine triad nucleotide-binding protein 1 / Protein kinase C-interacting protein 1
Function / homology
Function and homology information


purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / Regulation of MITF-M-dependent genes involved in apoptosis / intrinsic apoptotic signaling pathway by p53 class mediator / histone deacetylase complex / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity ...purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / Regulation of MITF-M-dependent genes involved in apoptosis / intrinsic apoptotic signaling pathway by p53 class mediator / histone deacetylase complex / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of calcium-mediated signaling / protein kinase C binding / cytoskeleton / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like superfamily
Similarity search - Domain/homology
Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Ju, C. / Ni, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of PKCi from Biortus
Authors: Wang, F. / Cheng, W. / Lv, Z. / Ju, C. / Ni, C.
History
DepositionNov 1, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenosine 5'-monophosphoramidase HINT1
B: Adenosine 5'-monophosphoramidase HINT1


Theoretical massNumber of molelcules
Total (without water)27,5142
Polymers27,5142
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-16 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.760, 75.047, 80.266
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: PRO / End label comp-ID: PRO / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 12 - 125 / Label seq-ID: 12 - 125

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein Adenosine 5'-monophosphoramidase HINT1 / Desumoylating isopeptidase HINT1 / Histidine triad nucleotide-binding protein 1 / Protein kinase C ...Desumoylating isopeptidase HINT1 / Histidine triad nucleotide-binding protein 1 / Protein kinase C inhibitor 1 / Protein kinase C-interacting protein 1 / PKCI-1


Mass: 13756.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT, PKCI1, PRKCNH1 / Production host: Escherichia coli (E. coli)
References: UniProt: P49773, Hydrolases; Acting on phosphorus-nitrogen bonds, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Na2tartrate, 0.1M Hepes pH7.0, 20% SOKALAN PA25 CL

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.1806 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1806 Å / Relative weight: 1
ReflectionResolution: 2.05→45.76 Å / Num. obs: 17997 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 9.9
Reflection shellResolution: 2.05→2.11 Å / Rmerge(I) obs: 0.942 / Num. unique obs: 1368

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→40.165 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.785 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / ESU R: 0.168 / ESU R Free: 0.156
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2172 1014 5.65 %
Rwork0.1705 16934 -
all0.173 --
obs-17948 99.939 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.127 Å2
Baniso -1Baniso -2Baniso -3
1--2.26 Å2-0 Å20 Å2
2--3.639 Å2-0 Å2
3----1.378 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1779 0 0 207 1986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121821
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161703
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.6472459
X-RAY DIFFRACTIONr_angle_other_deg0.4531.5843977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5235229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.295510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9210314
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.6641078
X-RAY DIFFRACTIONr_chiral_restr0.0680.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022067
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02341
X-RAY DIFFRACTIONr_nbd_refined0.1940.2387
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21637
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2896
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2996
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2154
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0110.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1330.28
X-RAY DIFFRACTIONr_nbd_other0.1660.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.215
X-RAY DIFFRACTIONr_mcbond_it2.1212.971922
X-RAY DIFFRACTIONr_mcbond_other2.1222.971921
X-RAY DIFFRACTIONr_mcangle_it2.9524.4421149
X-RAY DIFFRACTIONr_mcangle_other2.9514.4421150
X-RAY DIFFRACTIONr_scbond_it3.253.258899
X-RAY DIFFRACTIONr_scbond_other3.2493.258899
X-RAY DIFFRACTIONr_scangle_it4.6474.7741310
X-RAY DIFFRACTIONr_scangle_other4.6454.7741311
X-RAY DIFFRACTIONr_lrange_it5.87842.6742102
X-RAY DIFFRACTIONr_lrange_other5.77839.7572052
X-RAY DIFFRACTIONr_ncsr_local_group_10.1170.053288
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.116820.05009
12AX-RAY DIFFRACTIONLocal ncs0.116820.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.05-2.1030.228700.25312320.25113030.9490.93799.92330.225
2.103-2.1610.299690.24911960.25212650.9250.9411000.219
2.161-2.2230.27630.2311590.23212220.9370.951000.199
2.223-2.2910.255700.21411520.21612230.9560.95999.91820.182
2.291-2.3660.257530.20610910.20911440.940.9641000.175
2.366-2.4490.219430.18510930.18611360.9640.9711000.154
2.449-2.5410.245640.19210340.19510990.9660.97299.9090.156
2.541-2.6440.241520.1849910.18710430.9660.9761000.155
2.644-2.7610.266560.1799620.18410180.9630.9791000.151
2.761-2.8950.178550.1629170.1639720.9770.9821000.141
2.895-3.0510.242560.1688740.1739300.9660.9811000.148
3.051-3.2350.213680.1627970.1658650.9670.9841000.145
3.235-3.4570.216550.157750.1548300.9720.9851000.14
3.457-3.7320.168580.1437150.1457740.9830.98899.87080.137
3.732-4.0840.177430.1416780.1447210.9860.9881000.137
4.084-4.560.172360.1246220.1266590.9840.9999.84830.125
4.56-5.2550.194340.1185410.1215770.9860.99299.65340.122
5.255-6.4080.232310.1684800.1715120.9730.98399.80470.166
6.408-8.9490.269240.1873850.1914090.9590.9791000.19
8.949-40.1650.209140.2042410.2042570.9610.9799.22180.226

+
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