[English] 日本語
Yorodumi
- PDB-6sq7: Crystal structure of M. tuberculosis InhA in complex with NAD+ an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sq7
TitleCrystal structure of M. tuberculosis InhA in complex with NAD+ and 2-(4-chloro-3-nitrobenzoyl)benzoic acid
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / InhA / NADH-dependent enoyl-[acyl-carrier-protein] 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9FN / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 Å
AuthorsMendes, V. / Sabbah, M. / Coyne, A.G. / Abell, C. / Blundell, T.L.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme260872 United Kingdom
Bill & Melinda Gates FoundationOPP1158806 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Fragment-Based Design ofMycobacterium tuberculosisInhA Inhibitors.
Authors: Sabbah, M. / Mendes, V. / Vistal, R.G. / Dias, D.M.G. / Zahorszka, M. / Mikusova, K. / Kordulakova, J. / Coyne, A.G. / Blundell, T.L. / Abell, C.
History
DepositionSep 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6113
Polymers28,6421
Non-polymers9692
Water3,621201
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,44412
Polymers114,5674
Non-polymers3,8768
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_545x,x-y-1,-z+1/31
Buried area18980 Å2
ΔGint-127 kcal/mol
Surface area33100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.524, 97.524, 140.181
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

21A-487-

HOH

-
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: 28641.857 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: inhA, Rv1484, MTCY277.05 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-9FN / 2-(4-chloranyl-3-nitro-phenyl)carbonylbenzoic acid


Mass: 305.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8ClNO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES pH 7.0 0.1 M sodium acetate 25-30% PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.757→84.46 Å / Num. obs: 39915 / % possible obs: 100 % / Redundancy: 19.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.016 / Rrim(I) all: 0.068 / Net I/σ(I): 24.1
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.76-1.9619.20.657213551111230.9780.1530.6753.8
3.93-84.4617.30.0426720238890.9990.010.04361.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.12 Å84.46 Å
Translation6.12 Å84.46 Å

-
Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.2.17data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B35

2b35


Resolution: 1.76→84.458 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.62
RfactorNum. reflection% reflection
Rfree0.1636 1934 4.85 %
Rwork0.1562 --
obs0.1565 39842 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.35 Å2 / Biso mean: 37.2636 Å2 / Biso min: 21.42 Å2
Refinement stepCycle: final / Resolution: 1.76→84.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 65 201 2250
Biso mean--40.37 48.24 -
Num. residues----267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.76-1.80120.27871320.25282657
1.8012-1.84990.2581150.21282650
1.8499-1.90430.2211350.1892666
1.9043-1.96580.21431370.1662652
1.9658-2.0360.20521290.15642683
2.036-2.11760.19081430.15872649
2.1176-2.21390.16171480.15742671
2.2139-2.33070.16091330.15532685
2.3307-2.47670.18251280.15282702
2.4767-2.66790.18551500.1582686
2.6679-2.93640.16861580.15742708
2.9364-3.36130.16551270.15512747
3.3613-4.23490.13791460.14082788
4.2349-84.4580.14321530.15572964
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6550.2493-0.10680.92280.06471.31580.0093-0.01950.16490.0194-0.05310.0403-0.36830.0004-0.02040.2809-0.013-0.03930.1767-0.00070.229323.394-22.573824.3183
20.98550.03940.3570.89430.34491.39360.0098-0.17060.06230.1769-0.09550.0447-0.1025-0.05820.04090.2406-0.0616-0.0110.2442-0.01510.251632.2667-30.220234.684
32.9697-0.0514-0.56231.2708-0.12351.7186-0.0404-0.08580.28990.1970.0204-0.2497-0.34730.40150.03190.3955-0.1523-0.06090.27980.03090.341240.6009-16.48729.1226
42.97740.47750.58421.3298-0.08750.2804-0.0469-0.18810.43890.2031-0.0705-0.0654-0.46850.08520.03140.5498-0.118-0.06420.283-0.00380.338534.9177-7.763229.7782
56.892-0.5327-1.62482.528-0.77182.6654-0.14410.41310.873-0.17250.1954-0.0709-0.53490.0227-0.05190.6737-0.1369-0.09990.28890.05760.384530.3791-5.373317.1686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 83 through 182 )A83 - 182
2X-RAY DIFFRACTION2chain 'A' and (resid 183 through 269 )A183 - 269
3X-RAY DIFFRACTION3chain 'A' and (resid 3 through 31 )A3 - 31
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 67 )A32 - 67
5X-RAY DIFFRACTION5chain 'A' and (resid 68 through 82 )A68 - 82

+
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