[English] 日本語
Yorodumi
- PDB-7e48: Crystal structure of InhA in complex with 3-nitropropanoic acid i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7.0E+48
TitleCrystal structure of InhA in complex with 3-nitropropanoic acid inhibitor
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / ENOYL-ACP REDUCTASE / FAS-II ENOYL-ACP REDUCTASE / NADH- DEPENDENT 2-TRANS-ENOYL-ACP REDUCTASE
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / response to antibiotic / plasma membrane
Similarity search - Function
: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
3-NITROPROPANOIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSongsiriritthigul, C. / Hanwarinroj, C. / Suttipanta, N. / Kamsri, P. / Kittakoop, P. / Pungpo, P.
CitationJournal: Proteins / Year: 2022
Title: Inhibition of Mycobacterium tuberculosis InhA by 3-nitropropanoic acid.
Authors: Songsiriritthigul, C. / Hanwarinroj, C. / Pakamwong, B. / Srimanote, P. / Suttipanta, N. / Sureram, S. / Suttisintong, K. / Kamsri, P. / Punkvang, A. / Spencer, J. / Kittakoop, P. / Pungpo, P.
History
DepositionFeb 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 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: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,44113
Polymers114,2194
Non-polymers3,2229
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20460 Å2
ΔGint-125 kcal/mol
Surface area32680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.390, 96.390, 139.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-ACP reductase / FAS-II enoyl-ACP reductase / NADH-dependent 2-trans-enoyl-ACP reductase


Mass: 28554.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: inhA, Rv1484, MTCY277.05 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-3NP / 3-NITROPROPANOIC ACID


Mass: 119.076 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5NO4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: Purified protein incubated with NADH and 3NP in 5% (w/v) ethanol, 5% (w/v) MPD, 200mM sodium chloride, 100mM Tris-HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLRI / Beamline: BL7.2W / Wavelength: 1.24 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 22, 2018
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.5→28.76 Å / Num. obs: 50117 / % possible obs: 99.9 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.3
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 7302 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
MOSFLMiMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R9W

6r9w


Resolution: 2.5→28.76 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.034 / SU ML: 0.188 / Cross valid method: FREE R-VALUE / ESU R: 0.378 / ESU R Free: 0.237
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2195 2458 4.907 %
Rwork0.1847 47630 -
all0.186 --
obs-50088 99.916 %
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: 34.882 Å2
Baniso -1Baniso -2Baniso -3
1-0.081 Å20.041 Å20 Å2
2--0.081 Å20 Å2
3----0.263 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7953 0 214 369 8536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0138399
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177900
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.63711442
X-RAY DIFFRACTIONr_angle_other_deg1.0951.57518287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13951084
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.56821.809376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82151339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5981555
X-RAY DIFFRACTIONr_chiral_restr0.0380.21135
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029491
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021694
X-RAY DIFFRACTIONr_nbd_refined0.170.21889
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.27767
X-RAY DIFFRACTIONr_nbtor_refined0.1460.24009
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.23458
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2421
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0840.225
X-RAY DIFFRACTIONr_nbd_other0.2160.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.211
X-RAY DIFFRACTIONr_mcbond_it0.713.7184290
X-RAY DIFFRACTIONr_mcbond_other0.713.7184289
X-RAY DIFFRACTIONr_mcangle_it1.2565.5765361
X-RAY DIFFRACTIONr_mcangle_other1.2565.5775362
X-RAY DIFFRACTIONr_scbond_it0.7013.84109
X-RAY DIFFRACTIONr_scbond_other0.7013.84110
X-RAY DIFFRACTIONr_scangle_it1.2595.6456070
X-RAY DIFFRACTIONr_scangle_other1.2595.6466071
X-RAY DIFFRACTIONr_lrange_it2.73144.3169474
X-RAY DIFFRACTIONr_lrange_other2.69644.39433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.3211600.2943511X-RAY DIFFRACTION99.9728
2.565-2.6350.3161660.2783457X-RAY DIFFRACTION99.8622
2.635-2.7110.2881780.2573325X-RAY DIFFRACTION99.9715
2.711-2.7950.2921800.2523246X-RAY DIFFRACTION100
2.795-2.8860.3071720.2283132X-RAY DIFFRACTION99.9395
2.886-2.9880.2531720.2193017X-RAY DIFFRACTION99.9687
2.988-3.10.2661460.2042968X-RAY DIFFRACTION99.9679
3.1-3.2270.2211620.1942786X-RAY DIFFRACTION100
3.227-3.370.231510.1812691X-RAY DIFFRACTION100
3.37-3.5340.2121140.192632X-RAY DIFFRACTION100
3.534-3.7250.2011780.1722403X-RAY DIFFRACTION100
3.725-3.950.1651020.1582352X-RAY DIFFRACTION100
3.95-4.2220.149840.1452217X-RAY DIFFRACTION100
4.222-4.560.191960.1382065X-RAY DIFFRACTION100
4.56-4.9930.1851000.1371870X-RAY DIFFRACTION100
4.993-5.580.173840.1681702X-RAY DIFFRACTION100
5.58-6.4390.236850.1881493X-RAY DIFFRACTION100
6.439-7.8740.187460.1491271X-RAY DIFFRACTION100
7.874-11.0860.15550.108975X-RAY DIFFRACTION100
11.086-28.7630.213270.214517X-RAY DIFFRACTION94.6087

+
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