[English] 日本語
Yorodumi
- PDB-7dnq: Crystal structure of M.tuberculosis imidazole glycerol phosphate ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dnq
TitleCrystal structure of M.tuberculosis imidazole glycerol phosphate dehydratase in complex with an inhibitor
ComponentsImidazoleglycerol-phosphate dehydratase
KeywordsLYASE / Inhibitor
Function / homology
Function and homology information


imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Imidazoleglycerol-phosphate dehydratase signature 1. / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase, conserved site / Imidazole glycerol phosphate dehydratase domain superfamily / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase signature 2. / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
2-(1H-1,2,4-triazol-5-ylsulfanyl)ethanamine / : / Imidazoleglycerol-phosphate dehydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsTiwari, S. / Pal, R.K. / Biswal, B.K.
CitationJournal: To Be Published
Title: Crystal structure of M.tuberculosis imidazole glycerol phosphate dehydratase in complex with an inhibitor
Authors: Tiwari, S. / Pal, R.K. / Biswal, B.K.
History
DepositionDec 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Imidazoleglycerol-phosphate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0217
Polymers23,6341
Non-polymers3876
Water1,928107
1
A: Imidazoleglycerol-phosphate dehydratase
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)576,494168
Polymers567,20424
Non-polymers9,289144
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area104030 Å2
ΔGint-575 kcal/mol
Surface area122180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.100, 112.100, 112.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-303-

CL

21A-487-

HOH

31A-493-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Imidazoleglycerol-phosphate dehydratase / IGPD


Mass: 23633.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: hisB, Rv1601, MTCY336.03c / Production host: Mycolicibacterium smegmatis (bacteria)
References: UniProt: P9WML9, imidazoleglycerol-phosphate dehydratase

-
Non-polymers , 5 types, 113 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-HB3 / 2-(1H-1,2,4-triazol-5-ylsulfanyl)ethanamine


Mass: 144.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N4S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 20% PEG 1500, 0.2M sodium citrate tribasic dehydrate, 0.1M Tris HCL, pH 9.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.28→35 Å / Num. obs: 11541 / % possible obs: 99.9 % / Redundancy: 29.3 % / CC1/2: 0.94 / Net I/σ(I): 21.58
Reflection shellResolution: 2.28→2.36 Å / Num. unique obs: 1101 / CC1/2: 0.66

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GQU

4gqu


Resolution: 2.28→28.041 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.602 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / ESU R: 0.216 / ESU R Free: 0.185
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2099 587 5.086 %
Rwork0.1591 10954 -
all0.162 --
obs-11541 99.818 %
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: 28.777 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.28→28.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1459 0 17 107 1583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131501
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171377
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.6542039
X-RAY DIFFRACTIONr_angle_other_deg1.3251.5823162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.345189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28520.11488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02715227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9441516
X-RAY DIFFRACTIONr_chiral_restr0.0690.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
X-RAY DIFFRACTIONr_nbd_refined0.1910.2310
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.21248
X-RAY DIFFRACTIONr_nbtor_refined0.1530.2702
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2697
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0910.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1970.230
X-RAY DIFFRACTIONr_nbd_other0.2230.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.215
X-RAY DIFFRACTIONr_mcbond_it2.0262.876759
X-RAY DIFFRACTIONr_mcbond_other2.0222.87758
X-RAY DIFFRACTIONr_mcangle_it3.0914.301947
X-RAY DIFFRACTIONr_mcangle_other3.094.309948
X-RAY DIFFRACTIONr_scbond_it2.8263.252742
X-RAY DIFFRACTIONr_scbond_other2.8243.258743
X-RAY DIFFRACTIONr_scangle_it4.3794.721092
X-RAY DIFFRACTIONr_scangle_other4.3774.7261093
X-RAY DIFFRACTIONr_lrange_it5.77434.351616
X-RAY DIFFRACTIONr_lrange_other5.73134.2561602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.3390.301440.364779X-RAY DIFFRACTION99.1566
2.339-2.4030.301310.3781X-RAY DIFFRACTION100
2.403-2.4730.239420.236735X-RAY DIFFRACTION100
2.473-2.5490.221310.179736X-RAY DIFFRACTION100
2.549-2.6320.218360.179706X-RAY DIFFRACTION100
2.632-2.7250.254400.176686X-RAY DIFFRACTION100
2.725-2.8270.219430.173650X-RAY DIFFRACTION100
2.827-2.9430.18320.152642X-RAY DIFFRACTION100
2.943-3.0730.233300.153612X-RAY DIFFRACTION100
3.073-3.2230.215360.158591X-RAY DIFFRACTION100
3.223-3.3980.229270.143578X-RAY DIFFRACTION100
3.398-3.6030.253240.15539X-RAY DIFFRACTION100
3.603-3.8520.178250.128504X-RAY DIFFRACTION100
3.852-4.160.163320.115470X-RAY DIFFRACTION100
4.16-4.5570.159300.109435X-RAY DIFFRACTION100
4.557-5.0930.155220.112415X-RAY DIFFRACTION100
5.093-5.8790.238180.133362X-RAY DIFFRACTION100
5.879-7.1960.221180.15319X-RAY DIFFRACTION100
7.196-10.1550.217160.137257X-RAY DIFFRACTION100
10.155-280.223100.212157X-RAY DIFFRACTION92.2652

+
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