[English] 日本語
Yorodumi
- PDB-6m65: Crystal structure of Mycobacterium smegmatis MutT1 in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6m65
TitleCrystal structure of Mycobacterium smegmatis MutT1 in complex with GMPPNP (GDP)
ComponentsHydrolase, NUDIX family protein
KeywordsHYDROLASE / MsMutT1 / Nudix hydrolase / histidine phosphatase domain / Nucleotide pool sanitation enzyme / GMPPNP / Molecular aggregation / plasticity / enzyme action
Function / homology
Function and homology information


8-oxo-(d)GTP phosphatase / diadenosine hexaphosphate hydrolase (ATP-forming) / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase / 8-oxo-dGDP phosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA replication / DNA repair / metal ion binding
Similarity search - Function
Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / PYROPHOSPHATE 2- / 8-oxo-(d)GTP phosphatase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.44 Å
AuthorsRaj, P. / Karthik, S. / Arif, S.M. / Varshney, U. / Vijayan, M.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR20529/BRB/10/1525/2016 India
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1.
Authors: Raj, P. / Karthik, S. / Arif, S.M. / Varshney, U. / Vijayan, M.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Biochemical and structural studies of Mycobacterium smegmatis MutT1, a sanitization enzyme with unusual modes of association.
Authors: Arif, S.M. / Patil, A.G. / Varshney, U. / Vijayan, M.
#2: Journal: J. Struct. Biol. / Year: 2017
Title: Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1.
Authors: Arif, S.M. / Varshney, U. / Vijayan, M.
History
DepositionMar 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hydrolase, NUDIX family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,19910
Polymers38,1531
Non-polymers1,0469
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-13 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.560, 37.110, 44.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Hydrolase, NUDIX family protein


Mass: 38153.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: MSMEG_2390 / Production host: Escherichia coli (E. coli) / Strain (production host): JW0097 / References: UniProt: A0QUZ2

-
Non-polymers , 6 types, 439 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 4.6
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate, 30% w/v PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.44→43.63 Å / Num. obs: 59223 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rpim(I) all: 0.034 / Rrim(I) all: 0.092 / Rsym value: 0.086 / Net I/av σ(I): 6 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.44-1.5270.75185130.3020.8090.7599.7
1.52-1.617.20.4751.681020.1890.5110.47599.9
1.61-1.727.20.3222.376040.1280.3470.32299.9
1.72-1.867.20.2083.571260.0820.2240.208100
1.86-2.047.20.14565410.0550.150.14100
2.04-2.2870.0996.758120.040.1060.09997.8
2.28-2.637.10.0748.753300.030.080.07499.8
2.63-3.227.10.0698.645200.0270.0740.06999.9
3.22-4.5570.04312.935700.0170.0460.04399.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GG5

5gg5


Resolution: 1.44→36.76 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.361 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0675 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.071 / Details: Individual isotropic B-factor refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2148 2985 5 %RANDOM
Rwork0.1814 ---
obs0.1831 56131 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.52 Å2 / Biso mean: 16.954 Å2 / Biso min: 3.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0 Å2-0 Å2
2---0.05 Å20 Å2
3---0.66 Å2
Refinement stepCycle: final / Resolution: 1.44→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2258 0 64 441 2763
Biso mean--32.91 30.65 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132495
X-RAY DIFFRACTIONr_bond_other_d0.0340.0172329
X-RAY DIFFRACTIONr_angle_refined_deg2.081.6823416
X-RAY DIFFRACTIONr_angle_other_deg2.3751.5885377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.28519.862145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93915404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.431530
X-RAY DIFFRACTIONr_chiral_restr0.1080.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022836
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02558
LS refinement shellResolution: 1.44→1.477 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 196 -
Rwork0.289 4122 -
all-4318 -
obs--99.65 %

+
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