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- PDB-4oxn: Substrate-like binding mode of inhibitor PT155 to the Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 4oxn
TitleSubstrate-like binding mode of inhibitor PT155 to the Mycobacterium tuberculosis enoyl-ACP reductase InhA
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Bacterial fatty acid biosynthesis / conformational profile of enzyme-inhibitor complex / inhibition kinetics / substrate-binding loop refolding / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / 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 / fatty acid biosynthetic process ...enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / 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 / fatty acid biosynthetic process / 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-1S5 / 3,6,9,12,15-pentaoxaoctadecan-17-amine / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2926 Å
AuthorsLi, H.J. / Pan, P. / Lai, C.T. / Liu, N. / Garcia-Diaz, M. / Simmerling, C. / Tonge, P.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102864 United States
Department of Energy (DOE, United States) United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P41RR012408 United States
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: A Structural and Energetic Model for the Slow-Onset Inhibition of the Mycobacterium tuberculosis Enoyl-ACP Reductase InhA.
Authors: Li, H.J. / Lai, C.T. / Pan, P. / Yu, W. / Liu, N. / Bommineni, G.R. / Garcia-Diaz, M. / Simmerling, C. / Tonge, P.J.
History
DepositionFeb 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Refinement description
Revision 1.2Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 13, 2019Group: Data collection / Derived calculations / Refinement description
Category: diffrn_radiation / diffrn_source ...diffrn_radiation / diffrn_source / pdbx_struct_special_symmetry / software
Item: _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_source.pdbx_wavelength_list / _software.version
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / refine_hist
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,95217
Polymers61,4522
Non-polymers4,50015
Water2,486138
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)131,90434
Polymers122,9054
Non-polymers9,00030
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area27910 Å2
ΔGint-165 kcal/mol
Surface area31040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.952, 97.150, 187.009
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Components on special symmetry positions
IDModelComponents
11B-153-

ARG

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 30726.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT1531,MTCY277.05,Rv1484,inhA / Plasmid: peT-15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)

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Non-polymers , 6 types, 153 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-1S5 / 5-(4-amino-2-methylphenoxy)-2-hexyl-4-hydroxy-1-methylpyridinium


Mass: 314.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H26N2O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-2NV / 3,6,9,12,15-pentaoxaoctadecan-17-amine / Jeffamine ED-2001


Mass: 279.373 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C13H29NO5
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM HEPES pH 8.0, 32% Jeffamine ED-2001 pH 7.0 / PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9,1.1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 6, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
21.11
ReflectionResolution: 2.2→50 Å / Num. obs: 41571 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 26.38 Å2 / Rmerge(I) obs: 0.167 / Χ2: 1.166 / Net I/av σ(I): 13.554 / Net I/σ(I): 5.6 / Num. measured all: 305646
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.247.30.74720301.033100
2.24-2.287.30.68720621.054100
2.28-2.327.40.67820481.078100
2.32-2.377.40.57920541.111100
2.37-2.427.40.52720451.172100
2.42-2.487.40.49220591.185100
2.48-2.547.40.48220831.199100
2.54-2.617.40.420521.251100
2.61-2.697.40.34920411.239100
2.69-2.777.40.32620711.247100
2.77-2.877.40.2720781.254100
2.87-2.997.40.24320491.199100
2.99-3.127.40.22320791.227100
3.12-3.297.40.18420871.182100
3.29-3.497.40.15520711.16100
3.49-3.767.40.13720951.209100
3.76-4.147.40.12720911.237100
4.14-4.747.30.11221191.176100
4.74-5.977.30.10621301.163100
5.97-506.90.09222270.91999.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.14data extraction
REFMACrefinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X23

2x23


Resolution: 2.2926→44.476 Å / FOM work R set: 0.8554 / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2049 1838 5.09 %
Rwork0.1717 34283 -
obs0.1734 36121 98.34 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.45 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 84.31 Å2 / Biso mean: 29.75 Å2 / Biso min: 10.66 Å2
Baniso -1Baniso -2Baniso -3
1-4.062 Å2-0 Å2-0 Å2
2--4.659 Å2-0 Å2
3----8.721 Å2
Refinement stepCycle: final / Resolution: 2.2926→44.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 240 138 4247
Biso mean--41.47 29.65 -
Num. residues----529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084320
X-RAY DIFFRACTIONf_angle_d1.1325870
X-RAY DIFFRACTIONf_chiral_restr0.071644
X-RAY DIFFRACTIONf_plane_restr0.006738
X-RAY DIFFRACTIONf_dihedral_angle_d18.1811663
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2926-2.35460.22651330.17742297243088
2.3546-2.42390.22021280.17112645277399
2.4239-2.50210.24681540.17752600275499
2.5021-2.59150.26841420.17722634277699
2.5915-2.69530.22011210.18442660278199
2.6953-2.81790.26581460.18712570271698
2.8179-2.96650.23751350.18792650278598
2.9665-3.15230.20961400.18952628276898
3.1523-3.39560.20661440.16622659280399
3.3956-3.73720.19551550.160826742829100
3.7372-4.27750.1781450.153126962841100
4.2775-5.38780.17511540.152827162870100
5.3878-44.48430.18621410.191628542995100
Refinement TLS params.Method: refined / Origin x: -7.5593 Å / Origin y: 11.2098 Å / Origin z: 23.5271 Å
111213212223313233
T0.1846 Å2-0.0345 Å2-0.0063 Å2-0.1434 Å2-0.0056 Å2--0.1183 Å2
L1.1173 °2-0.3405 °20.0809 °2-1.0567 °2-0.038 °2--1.0275 °2
S0.0407 Å °0.0197 Å °-0.1127 Å °-0.1052 Å °-0.0562 Å °0.1074 Å °0.2063 Å °-0.119 Å °0.0137 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 269
2X-RAY DIFFRACTION1allB2 - 301
3X-RAY DIFFRACTION1allA301 - 307
4X-RAY DIFFRACTION1allB301 - 308
5X-RAY DIFFRACTION1allA401 - 462
6X-RAY DIFFRACTION1allB401 - 476

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