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- PDB-6ki9: Apo structure of FabMG, novel types of Enoyl-acyl carrier protein... -

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Basic information

Entry
Database: PDB / ID: 6ki9
TitleApo structure of FabMG, novel types of Enoyl-acyl carrier protein reductase
ComponentsFabMG, novel types of Enoyl-acyl carrier protein reductase
KeywordsOXIDOREDUCTASE / Enoyl-acyl carrier protein reductase / FabMG
Function / homology: / Enoyl-acyl carrier protein reductase FabMG / nucleotide binding / Uncharacterized protein
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.64 Å
AuthorsKim, S. / Rhee, S.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Rural Development AdministrationPJ01325801 Korea, Republic Of
National Research Foundation (NRF, Korea)2017R1A2B4002860 Korea, Republic Of
CitationJournal: Febs J. / Year: 2020
Title: A triclosan-resistance protein from the soil metagenome is a novel enoyl-acyl carrier protein reductase: Structure-guided functional analysis.
Authors: Kim, S.H. / Khan, R. / Choi, K. / Lee, S.W. / Rhee, S.
History
DepositionJul 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 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 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FabMG, novel types of Enoyl-acyl carrier protein reductase
B: FabMG, novel types of Enoyl-acyl carrier protein reductase
C: FabMG, novel types of Enoyl-acyl carrier protein reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,77523
Polymers148,2703
Non-polymers1,50620
Water16,538918
1
A: FabMG, novel types of Enoyl-acyl carrier protein reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,11410
Polymers49,4231
Non-polymers6919
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FabMG, novel types of Enoyl-acyl carrier protein reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9908
Polymers49,4231
Non-polymers5677
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FabMG, novel types of Enoyl-acyl carrier protein reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6725
Polymers49,4231
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.862, 137.005, 156.862
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETARGARGchain 'A'AA1 - 561 - 56
12ASNASNGLUGLUchain 'A'AA60 - 44060 - 440
23METMETARGARGchain 'B'BB1 - 561 - 56
24ASNASNGLUGLUchain 'B'BB60 - 44060 - 440

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Components

#1: Protein FabMG, novel types of Enoyl-acyl carrier protein reductase


Mass: 49423.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1C9HA64
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 918 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-tris (pH 6.5), 23% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 168488 / % possible obs: 99.9 % / Redundancy: 14 % / Biso Wilson estimate: 22.0727481816 Å2 / CC1/2: 0.999 / Net I/σ(I): 32.8
Reflection shellResolution: 1.644→1.703 Å / Num. unique obs: 16628 / CC1/2: 0.841

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.64→26.7277265571 Å / SU ML: 0.174965452937 / Cross valid method: NONE / σ(F): 1.33792973872 / Phase error: 25.740589025
RfactorNum. reflection% reflection
Rfree0.241672819757 2000 1.18795179292 %
Rwork0.216979745648 --
obs0.217272860095 168357 99.9246219226 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.6359567753 Å2
Refinement stepCycle: LAST / Resolution: 1.64→26.7277265571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9587 0 98 918 10603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004504849057999858
X-RAY DIFFRACTIONf_angle_d0.8736121387513280
X-RAY DIFFRACTIONf_chiral_restr0.03374288337151468
X-RAY DIFFRACTIONf_plane_restr0.004669911971981703
X-RAY DIFFRACTIONf_dihedral_angle_d12.40021538593607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.68170.3206280618141410.28596916802411754X-RAY DIFFRACTION99.848904558
1.6817-1.72710.284821874681420.27350539080611765X-RAY DIFFRACTION99.9580255205
1.7271-1.77790.3375980290331410.27807774091511776X-RAY DIFFRACTION99.9496770947
1.7779-1.83530.2683907211131420.26118406366211732X-RAY DIFFRACTION99.9494949495
1.8353-1.90090.2714176423021410.25778022699711785X-RAY DIFFRACTION99.974851203
1.9009-1.9770.2868426703291420.25226398901311818X-RAY DIFFRACTION99.991639495
1.977-2.06690.2700985286251430.24174052896611862X-RAY DIFFRACTION99.9916708313
2.0669-2.17580.283679012491420.22885527401211824X-RAY DIFFRACTION100
2.1758-2.31210.2505081652241430.23155720752511847X-RAY DIFFRACTION99.991660412
2.3121-2.49050.2630240436931420.22966258811871X-RAY DIFFRACTION100
2.4905-2.74090.2467617517281440.22451214081111937X-RAY DIFFRACTION99.9917232246
2.7409-3.1370.2714360842051430.22144876045311957X-RAY DIFFRACTION99.983473806
3.137-3.95020.1988239420691450.19210843065612070X-RAY DIFFRACTION99.9918140144
3.9502-26.7270.2018091493691490.18096159926112359X-RAY DIFFRACTION99.3486894361
Refinement TLS params.Method: refined / Origin x: -15.0214671035 Å / Origin y: 21.2549402238 Å / Origin z: 32.0679171839 Å
111213212223313233
T0.150990816777 Å20.00513040573484 Å20.00319246288151 Å2-0.162331556815 Å20.0516506590137 Å2--0.240014270466 Å2
L0.0574361386837 °20.0546377795978 °2-0.0351505485932 °2-0.113321388837 °2-0.146351156737 °2--0.34338646088 °2
S0.00624738891465 Å °-0.0280643155341 Å °-0.0297520082378 Å °0.0854838496624 Å °0.0157575384023 Å °-0.00833413707392 Å °-0.00958346178226 Å °-0.0260695183182 Å °-0.0253256024526 Å °
Refinement TLS groupSelection details: all

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