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- PDB-6kia: NADH bound structure of FabMG, novel type of Enoyl-acyl carrier p... -

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Basic information

Entry
Database: PDB / ID: 6kia
TitleNADH bound structure of FabMG, novel type of Enoyl-acyl carrier protein reductase
ComponentsEnoyl-acyl carrier protein reductase
KeywordsOXIDOREDUCTASE / Enoyl-acyl carrier protein reductase / FabMG
Function / homology1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / SIR2_2 domain-containing protein
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5979826945 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: Enoyl-acyl carrier protein reductase
B: Enoyl-acyl carrier protein reductase
C: Enoyl-acyl carrier protein reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,2666
Polymers148,2703
Non-polymers1,9963
Water15,547863
1
A: Enoyl-acyl carrier protein reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0892
Polymers49,4231
Non-polymers6651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-9 kcal/mol
Surface area18510 Å2
MethodPISA
2
B: Enoyl-acyl carrier protein reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0892
Polymers49,4231
Non-polymers6651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-9 kcal/mol
Surface area18360 Å2
MethodPISA
3
C: Enoyl-acyl carrier protein reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0892
Polymers49,4231
Non-polymers6651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-9 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.558, 138.219, 157.408
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
31

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
11METMETPHEPHEchain 'A'AA1 - 161 - 16
12VALVALGLYGLYchain 'A'AA21 - 5421 - 54
13ASNASNARGARGchain 'A'AA60 - 6360 - 63
14GLYGLYILEILEchain 'A'AA78 - 8178 - 81
15ASNASNVALVALchain 'A'AA83 - 8483 - 84
16LEULEUPROPROchain 'A'AA86 - 9586 - 95
17GLUGLUCYSCYSchain 'A'AA98 - 12698 - 126
18ALAALAARGARGchain 'A'AA128 - 133128 - 133
19LYSLYSVALVALchain 'A'AA135 - 138135 - 138
110ALAALASERSERchain 'A'AA155 - 220155 - 220
111ALAALAGLUGLUchain 'A'AA222 - 228222 - 228
112TYRTYRLYSLYSchain 'A'AA236 - 278236 - 278
113GLYGLYGLUGLUchain 'A'AA280 - 316280 - 316
114GLNGLNCYSCYSchain 'A'AA325 - 329325 - 329
115THRTHRHISHISchain 'A'AA338 - 387338 - 387
116ALAALAHISHISchain 'A'AA392 - 437392 - 437
217METMETPHEPHEchain 'B'BB1 - 161 - 16
218VALVALGLYGLYchain 'B'BB21 - 5421 - 54
219ASNASNARGARGchain 'B'BB60 - 6360 - 63
220GLYGLYILEILEchain 'B'BB78 - 8178 - 81
221ASNASNVALVALchain 'B'BB83 - 8483 - 84
222LEULEUPROPROchain 'B'BB86 - 9586 - 95
223GLUGLUCYSCYSchain 'B'BB98 - 12698 - 126
224ALAALAARGARGchain 'B'BB128 - 133128 - 133
225LYSLYSVALVALchain 'B'BB135 - 138135 - 138
226ALAALASERSERchain 'B'BB155 - 220155 - 220
227ALAALAGLUGLUchain 'B'BB222 - 228222 - 228
228TYRTYRLYSLYSchain 'B'BB236 - 278236 - 278
229GLYGLYGLUGLUchain 'B'BB280 - 316280 - 316
230GLNGLNCYSCYSchain 'B'BB325 - 329325 - 329
231THRTHRHISHISchain 'B'BB338 - 387338 - 387
232ALAALAHISHISchain 'B'BB392 - 437392 - 437
333METMETPHEPHEchain 'C'CC1 - 161 - 16
334VALVALGLYGLYchain 'C'CC21 - 5421 - 54
335ASNASNARGARGchain 'C'CC60 - 6360 - 63
336GLYGLYILEILEchain 'C'CC78 - 8178 - 81
337ASNASNVALVALchain 'C'CC83 - 8483 - 84
338LEULEUPROPROchain 'C'CC86 - 9586 - 95
339GLUGLUCYSCYSchain 'C'CC98 - 12698 - 126
340ALAALAARGARGchain 'C'CC128 - 133128 - 133
341LYSLYSVALVALchain 'C'CC135 - 138135 - 138
342ALAALASERSERchain 'C'CC155 - 220155 - 220
343ALAALAGLUGLUchain 'C'CC222 - 228222 - 228
344TYRTYRLYSLYSchain 'C'CC236 - 278236 - 278
345GLYGLYGLUGLUchain 'C'CC280 - 316280 - 316
346GLNGLNCYSCYSchain 'C'CC325 - 329325 - 329
347THRTHRHISHISchain 'C'CC338 - 387338 - 387
348ALAALAHISHISchain 'C'CC392 - 437392 - 437

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Components

#1: Protein Enoyl-acyl carrier protein reductase / / FabMG


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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 863 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Bis-Tris(pH 6.5) and 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: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 183554 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 22.5843519283 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Net I/av σ(I): 18.56 / Net I/σ(I): 18.5641
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 1.718 / Mean I/σ(I) obs: 0.91 / Num. unique obs: 18110 / CC1/2: 0.413

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5979826945→29.8088480406 Å / SU ML: 0.22355122888 / Cross valid method: NONE / σ(F): 1.32549687557 / Phase error: 27.9406550745
RfactorNum. reflection% reflection
Rfree0.25863972043 1987 1.09312164073 %
Rwork0.224008913351 179786 -
obs0.224383768772 181773 99.0232395977 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.0508075412 Å2
Refinement stepCycle: LAST / Resolution: 1.5979826945→29.8088480406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9669 0 132 863 10664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007932757148519995
X-RAY DIFFRACTIONf_angle_d1.1815984833613531
X-RAY DIFFRACTIONf_chiral_restr0.05316095538391513
X-RAY DIFFRACTIONf_plane_restr0.006533221160331723
X-RAY DIFFRACTIONf_dihedral_angle_d13.32671012233605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.598-1.63790.386267092891400.33205227108212620X-RAY DIFFRACTION98.2520982521
1.6379-1.68220.3162986042351410.29953698212612796X-RAY DIFFRACTION99.8071285295
1.6822-1.73170.3055717827931430.27756292272612817X-RAY DIFFRACTION99.8613037448
1.7317-1.78760.3202237301981420.26451591673712842X-RAY DIFFRACTION99.9461165422
1.7876-1.85150.2608015164041420.26295105026912846X-RAY DIFFRACTION99.8232265007
1.8515-1.92560.3906018039551420.37835709115712668X-RAY DIFFRACTION98.1910164035
1.9256-2.01320.3491577906871400.26999306763112797X-RAY DIFFRACTION99.5077301746
2.0132-2.11930.2209029080661430.21908940606312902X-RAY DIFFRACTION99.7400412876
2.1193-2.25210.2913060246871410.2588938549712700X-RAY DIFFRACTION98.2854955989
2.2521-2.42590.3011352876221360.24734094825312689X-RAY DIFFRACTION97.7291777795
2.4259-2.66990.2550588977381420.21662947167212941X-RAY DIFFRACTION99.68
2.6699-3.05590.2195819931811450.21033619074413000X-RAY DIFFRACTION99.605971054
3.0559-3.84880.2487560763411450.18524620962513073X-RAY DIFFRACTION99.4806954166
3.8488-29.80.2130211693741450.1859959338413095X-RAY DIFFRACTION96.5436779933
Refinement TLS params.Method: refined / Origin x: -15.4902999696 Å / Origin y: 22.3248696794 Å / Origin z: 31.654328472 Å
111213212223313233
T0.13579946301 Å20.00911572628517 Å20.012352505718 Å2-0.234049889136 Å20.0569311446211 Å2--0.269619537206 Å2
L0.0789678952009 °2-0.0219963903254 °2-0.015951023182 °2-0.26670197045 °2-0.0389557712255 °2--0.124799730939 °2
S-0.0166795782314 Å °-0.0672644134411 Å °-0.0366450982623 Å °0.11739770867 Å °0.0122883422945 Å °0.0239798521048 Å °0.00358792013975 Å °-0.00463836053965 Å °0.00706790132173 Å °
Refinement TLS groupSelection details: all

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