[English] 日本語
Yorodumi
- PDB-5qha: PanDDA analysis group deposition of models with modelled events (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5qha
TitlePanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with PCM-0102951
ComponentsPeroxisomal coenzyme A diphosphatase NUDT7
KeywordsHYDROLASE / PanDDA / SGC - Diamond I04-1 fragment screening / NUDIX domain / XChemExplorer
Function / homology
Function and homology information


butyryl-CoA catabolic process / propionyl-CoA metabolic process / propionyl-CoA catabolic process / medium-chain fatty-acyl-CoA catabolic process / malonyl-CoA catabolic process / Peroxisomal lipid metabolism / coenzyme A diphosphatase activity / coenzyme A catabolic process / acetyl-CoA catabolic process / succinyl-CoA catabolic process ...butyryl-CoA catabolic process / propionyl-CoA metabolic process / propionyl-CoA catabolic process / medium-chain fatty-acyl-CoA catabolic process / malonyl-CoA catabolic process / Peroxisomal lipid metabolism / coenzyme A diphosphatase activity / coenzyme A catabolic process / acetyl-CoA catabolic process / succinyl-CoA catabolic process / nucleoside diphosphate metabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / peroxisomal matrix / brown fat cell differentiation / Peroxisomal protein import / peroxisome / manganese ion binding / magnesium ion binding / cytosol
Similarity search - Function
NUDIX hydrolase, NudL, conserved site / Nudix CoA signature. / Coenzyme A pyrophosphatase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / Chem-H3D / Peroxisomal coenzyme A diphosphatase NUDT7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.57 Å
AuthorsKrojer, T. / Talon, R. / Fairhead, M. / Diaz Saez, L. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Ruda, G.F. ...Krojer, T. / Talon, R. / Fairhead, M. / Diaz Saez, L. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Ruda, G.F. / Szommer, T. / Srikannathasan, V. / Elkins, J. / Spencer, J. / London, N. / Nelson, A. / Brennan, P.E. / Huber, K. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Krojer, T. / Talon, R. / Fairhead, M. / Diaz Saez, L. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Ruda, G.F. / Szommer, T. / Srikannathasan, V. / Elkins, ...Authors: Krojer, T. / Talon, R. / Fairhead, M. / Diaz Saez, L. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Ruda, G.F. / Szommer, T. / Srikannathasan, V. / Elkins, J. / Spencer, J. / London, N. / Nelson, A. / Brennan, P.E. / Huber, K. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
History
DepositionSep 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peroxisomal coenzyme A diphosphatase NUDT7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5774
Polymers22,1981
Non-polymers3793
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-0 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.800, 123.800, 41.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

-
Components

#1: Protein Peroxisomal coenzyme A diphosphatase NUDT7 / Nucleoside diphosphate-linked moiety X motif 7 / Nudix motif 7


Mass: 22197.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT7 / Production host: Escherichia coli (E. coli)
References: UniProt: P0C024, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-H3D / N-[1-(2,3-dihydro-1,4-benzodioxin-6-yl)cyclopentyl]acetamide


Mass: 261.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 4.09 Å3/Da / Density % sol: 69.94 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.57→53.61 Å / Num. obs: 50185 / % possible obs: 99.3 % / Redundancy: 7.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.043 / Rrim(I) all: 0.129 / Net I/σ(I): 8.2 / Num. measured all: 388598 / Scaling rejects: 15
Reflection shellResolution: 1.57→1.61 Å / Redundancy: 5.8 % / Rmerge(I) obs: 2.865 / Num. measured all: 20976 / Num. unique all: 3598 / CC1/2: 0.534 / Rpim(I) all: 1.28 / Rrim(I) all: 3.147 / Net I/σ(I) obs: 0.5 / % possible all: 97.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5T3P

5t3p


Resolution: 1.57→107.21 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 6.081 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2425 4.9 %RANDOM
Rwork0.194 ---
obs0.196 47257 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.66 Å2 / Biso mean: 30.8 Å2 / Biso min: 14.37 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å2-0.82 Å20 Å2
2---1.63 Å20 Å2
3---5.3 Å2
Refinement stepCycle: final / Resolution: 1.57→107.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1449 0 27 175 1651
Biso mean--49.06 46.99 -
Num. residues----185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191539
X-RAY DIFFRACTIONr_bond_other_d0.0020.021430
X-RAY DIFFRACTIONr_angle_refined_deg1.8132.0032100
X-RAY DIFFRACTIONr_angle_other_deg1.05733326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2975189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.91824.47867
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12115246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.049157
X-RAY DIFFRACTIONr_chiral_restr0.1130.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211702
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02291
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_it4.7272.729755
X-RAY DIFFRACTIONr_mcbond_other4.7242.729756
X-RAY DIFFRACTIONr_mcangle_it5.7534.087944
X-RAY DIFFRACTIONMAIN-CHAIN ANGLE OTHER ATOMS (A**2)
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONSIDE-CHAIN BOND OTHER ATOMS (A**2)
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONSIDE-CHAIN ANGLE OTHER ATOMS (A**2)
X-RAY DIFFRACTIONLONG RANGE B REFINED ATOMS (A**2)
X-RAY DIFFRACTIONLONG RANGE B OTHER ATOMS (A**2)
X-RAY DIFFRACTIONr_rigid_bond_restr2.77932967
X-RAY DIFFRACTIONr_sphericity_free45.604597
X-RAY DIFFRACTIONr_sphericity_bonded22.81753008
LS refinement shellResolution: 1.57→1.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.514 153 -
Rwork0.491 3339 -
all-3492 -
obs--94.63 %

+
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://pdbjlvh1.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