[English] 日本語
Yorodumi
- PDB-1q74: The Crystal Structure of 1D-myo-inositol 2-acetamido-2-deoxy-alph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1q74
TitleThe Crystal Structure of 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside Deacetylase (MshB)
Components1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside Deacetylase (MshB)
KeywordsHYDROLASE / rossmann fold / zinc aminohydrolase / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


N-acetyl-1-D-myo-inositol-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase / N-acetylglucosaminylinositol deacetylase activity / mycothiol biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / zinc ion binding / plasma membrane
Similarity search - Function
Mycothiol biosynthesis protein, MshB / LmbE-like / N-acetylglucosaminyl phosphatidylinositol deacetylase-related / Putative deacetylase LmbE-like domain superfamily / GlcNAc-PI de-N-acetylase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase / 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsMaynes, J.T. / Garen, C. / Cherney, M.M. / Newton, G. / Arad, D. / Av-Gay, Y. / Fahey, R.C. / James, M.N. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The Crystal Structure of 1-D-myo-Inositol 2-Acetamido-2-deoxy-alpha-D-glucopyranoside Deacetylase (MshB) from Mycobacterium tuberculosis Reveals a Zinc Hydrolase with a Lactate Dehydrogenase Fold.
Authors: Maynes, J.T. / Garen, C. / Cherney, M.M. / Newton, G. / Arad, D. / Av-Gay, Y. / Fahey, R.C. / James, M.N.
History
DepositionAug 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside Deacetylase (MshB)
B: 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside Deacetylase (MshB)
C: 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside Deacetylase (MshB)
D: 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside Deacetylase (MshB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,7259
Polymers127,1094
Non-polymers6165
Water13,691760
1
A: 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside Deacetylase (MshB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1973
Polymers31,7771
Non-polymers4202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside Deacetylase (MshB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8432
Polymers31,7771
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside Deacetylase (MshB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8432
Polymers31,7771
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside Deacetylase (MshB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8432
Polymers31,7771
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.794, 73.964, 85.587
Angle α, β, γ (deg.)102.09, 108.16, 97.18
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside Deacetylase (MshB)


Mass: 31777.230 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv1170 / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O50426, UniProt: P9WJN3*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 760 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG4000, 50mM Tris-HCl, 0.1M Mg(NO3)2, 6% 1,6-hexanediol and 10% ethyleneglycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 %PEG40001reservoir
250 mMTris-HCl1reservoirpH8.0
30.1 M1reservoirMg(NO3)2
46 %1,6-hexanediol1reservoir
510 %ethylene glycol1reservoir
66 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2001
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 1331320 / Num. obs: 517484 / % possible obs: 96.3 % / Observed criterion σ(F): 4.8 / Observed criterion σ(I): 2.2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.2 / Num. unique all: 19275 / Rsym value: 0.296 / % possible all: 95.3
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 134270 / Num. measured all: 1281662 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Lowest resolution: 1.79 Å / % possible obs: 94.7 %

-
Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→19.84 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.227 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 4.8 / σ(I): 2.2 / ESU R: 0.108 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22787 6745 5 %RANDOM
Rwork0.1944 ---
all0.19608 1331320 --
obs0.19608 127442 96.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8364 0 28 760 9152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0218578
X-RAY DIFFRACTIONr_bond_other_d0.0040.027783
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.93411714
X-RAY DIFFRACTIONr_angle_other_deg1.468317892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.93731106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.638151271
X-RAY DIFFRACTIONr_chiral_restr0.1160.21320
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.029838
X-RAY DIFFRACTIONr_gen_planes_other0.0170.021797
X-RAY DIFFRACTIONr_nbd_refined0.1930.31652
X-RAY DIFFRACTIONr_nbd_other0.1330.37404
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.51567
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.10.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1520.371
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3160.559
X-RAY DIFFRACTIONr_mcbond_it1.1081.55526
X-RAY DIFFRACTIONr_mcangle_it1.90728771
X-RAY DIFFRACTIONr_scbond_it2.94333052
X-RAY DIFFRACTIONr_scangle_it4.6944.52943
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 497
Rwork0.257 9167
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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