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- PDB-4w9n: Enoyl-acyl carrier protein-reductase domain from human fatty acid... -

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Basic information

Entry
Database: PDB / ID: 4w9n
TitleEnoyl-acyl carrier protein-reductase domain from human fatty acid synthase complexed with triclosan
Components(Enoyl-[acyl-carrier-protein] ...) x 2
KeywordsOXIDOREDUCTASE / fatty acid synthase / fatty acid metabolism / NADPH-dependent / enoyl reductase
Function / homology
Function and homology information


fatty-acid synthase system / : / : / : / ether lipid biosynthetic process / Vitamin B5 (pantothenate) metabolism / : / neutrophil differentiation / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / glandular epithelial cell development ...fatty-acid synthase system / : / : / : / ether lipid biosynthetic process / Vitamin B5 (pantothenate) metabolism / : / neutrophil differentiation / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / glandular epithelial cell development / glycogen granule / establishment of endothelial intestinal barrier / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / : / oleoyl-[acyl-carrier-protein] hydrolase / Fatty acyl-CoA biosynthesis / fatty acyl-[ACP] hydrolase activity / modulation by host of viral process / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / ChREBP activates metabolic gene expression / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / beta-ketoacyl-[acyl-carrier-protein] synthase I / mammary gland development / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid synthase activity / phosphopantetheine binding / monocyte differentiation / 3-oxoacyl-[acyl-carrier-protein] synthase activity / cellular response to interleukin-4 / Activation of gene expression by SREBF (SREBP) / fatty acid metabolic process / fatty acid biosynthetic process / osteoblast differentiation / melanosome / inflammatory response / cadherin binding / Golgi apparatus / RNA binding / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Fatty acid synthase, pseudo-KR domain / Methyltransferase type 12 / Methyltransferase domain / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain ...: / Fatty acid synthase, pseudo-KR domain / Methyltransferase type 12 / Methyltransferase domain / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / TRICLOSAN / Fatty acid synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsSippel, K.H. / Vyas, N.K. / Sankaran, B. / Quiocho, F.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationQ-0581 United States
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal structure of the human Fatty Acid synthase enoyl-acyl carrier protein-reductase domain complexed with triclosan reveals allosteric protein-protein interface inhibition.
Authors: Sippel, K.H. / Vyas, N.K. / Zhang, W. / Sankaran, B. / Quiocho, F.A.
History
DepositionAug 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_related / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_related.content_type / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_keywords.text

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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
D: Enoyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,29519
Polymers147,1704
Non-polymers1,12515
Water9,422523
1
A: Enoyl-[acyl-carrier-protein] reductase
B: Enoyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,14910
Polymers73,5562
Non-polymers5938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-88 kcal/mol
Surface area25240 Å2
MethodPISA
2
C: Enoyl-[acyl-carrier-protein] reductase
D: Enoyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1469
Polymers73,6142
Non-polymers5327
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-72 kcal/mol
Surface area25250 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10810 Å2
ΔGint-176 kcal/mol
Surface area47710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.564, 75.834, 83.264
Angle α, β, γ (deg.)65.380, 88.870, 65.080
Int Tables number1
Space group name H-MP1

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Components

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Enoyl-[acyl-carrier-protein] ... , 2 types, 4 molecules ABDC

#1: Protein Enoyl-[acyl-carrier-protein] reductase


Mass: 36778.012 Da / Num. of mol.: 3 / Fragment: unp residues 1529-1867
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FASN, FAS / Plasmid: ptyb21 / Production host: Escherichia coli (E. coli)
References: UniProt: P49327, [acyl-carrier-protein] S-malonyltransferase
#2: Protein Enoyl-[acyl-carrier-protein] reductase


Mass: 36836.047 Da / Num. of mol.: 1 / Fragment: unp residues 1529-1867 / Mutation: C1548(CSS)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FASN, FAS / Plasmid: ptyb21 / Production host: Escherichia coli (E. coli)
References: UniProt: P49327, [acyl-carrier-protein] S-malonyltransferase

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Non-polymers , 5 types, 538 molecules

#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H7Cl3O2 / Comment: antifungal, antibiotic, detergent*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM NADP+ and 2 mM triclosan cocrystallized with 2.625 M sodium chloride, 100 mM imidazole pH 7.5, microseeded

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEApr 15, 2014
RIGAKU RAXIS IV++2IMAGE PLATEMay 8, 2014
RadiationMonochromator: VeriMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 6.2 % / Number: 695699 / Rmerge(I) obs: 0.195 / D res high: 1.84 Å / D res low: 28.43 Å / Num. obs: 112996 / % possible obs: 95.9 / Rejects: 52
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
1.841.8711.5783.7
10.0828.4310.1127
ReflectionResolution: 1.84→28.43 Å / Num. obs: 112996 / % possible obs: 95.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 24.65 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.08 / Net I/σ(I): 8.3 / Num. measured all: 695699 / Scaling rejects: 52
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.84-1.873.71.5780.81838449250.5250.92784.5
10.08-28.4370.11229.347816810.9970.04494.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1772)refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W82

4w82


Resolution: 1.84→26.428 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 29.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 6196 2.76 %Random
Rwork0.2056 218144 --
obs0.2064 112170 95.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.8 Å2 / Biso mean: 36.24 Å2 / Biso min: 13.61 Å2
Refinement stepCycle: final / Resolution: 1.84→26.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9360 0 83 523 9966
Biso mean--35.91 37.57 -
Num. residues----1262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219044
X-RAY DIFFRACTIONf_angle_d0.63434254
X-RAY DIFFRACTIONf_chiral_restr0.0281526
X-RAY DIFFRACTIONf_plane_restr0.0023014
X-RAY DIFFRACTIONf_dihedral_angle_d10.1385222
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.86090.31561900.29966352654283
1.8609-1.88280.36871610.30256239640082
1.8828-1.90580.34651730.30346370654382
1.9058-1.92990.33962060.29456245645184
1.9299-1.95530.34252050.28427235744094
1.9553-1.9820.31571860.28147275746195
1.982-2.01030.34211890.2797323751296
2.0103-2.04030.29062130.27687273748695
2.0403-2.07220.36841970.26797252744995
2.0722-2.10620.33951980.26277336753496
2.1062-2.14250.26672360.25277350758696
2.1425-2.18140.24122100.24557338754896
2.1814-2.22330.26562250.23257416764196
2.2233-2.26870.25882180.22987332755097
2.2687-2.3180.25952030.22527364756797
2.318-2.37190.24992130.21357474768797
2.3719-2.43120.27132070.2177377758497
2.4312-2.49690.2662200.21627370759097
2.4969-2.57030.27572120.21157457766997
2.5703-2.65320.26972250.21597456768198
2.6532-2.74790.21211910.21237545773698
2.7479-2.85780.2772090.22457500770998
2.8578-2.98770.25252260.21417486771298
2.9877-3.1450.26371980.21217485768398
3.145-3.34160.20452000.19787523772399
3.3416-3.59910.19952220.1867577779999
3.5991-3.96020.18382190.16267515773499
3.9602-4.53070.16382020.14957586778899
4.5307-5.69880.17742200.15587532775299
5.6988-26.43110.19112220.19097561778399
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)
12.674-0.14640.542.25680.64561.90910.0126-0.01390.0551-0.0625-0.01140.1510.0159-0.2493-0.00010.1848-0.03020.01960.20180.02290.1689-46.4434-10.195918.9411
21.5672-0.26591.44711.42840.0352.31840.0825-0.0603-0.1940.1530.0479-0.07060.19610.05940.00240.1983-0.02070.02160.18640.02280.1895-24.6245-9.400236.6697
31.7114-0.06620.28240.87120.25561.0610.05020.0476-0.36440.00170.0805-0.07280.20540.03640.00530.2502-0.03840.02650.17930.02510.201-36.9298-16.263820.9248
41.365-1.07541.06061.82320.00641.9835-0.277-0.27160.25450.5375-0.0412-0.2457-0.32030.0165-0.00170.3420.0248-0.06980.3064-0.02370.284-12.806916.747564.2389
52.3534-0.66341.53822.4345-0.31881.8848-0.1881-0.10950.27810.1006-0.05810.2037-0.2666-0.2371-0.01870.24150.04070.02940.223-0.03190.1942-30.357618.871544.5855
61.9294-1.20360.49981.4813-0.65042.2393-0.9194-0.07220.86550.6918-0.0091-0.5911-0.9372-0.1429-1.93210.54730.1594-0.09320.1547-0.24880.1655-18.48425.158457.1103
71.4916-0.77540.8041.74110.51591.77680.03580.3655-0.0937-0.30270.0666-0.02390.22190.084600.3169-0.0177-0.01080.2958-0.01210.2065-38.147910.5938-14.3644
82.06050.4311.35652.45741.0361.9007-0.0772-0.0230.2897-0.0318-0.034-0.0304-0.1459-0.012-0.00580.20.00170.04120.1840.03350.1685-30.149426.4485.1221
91.17860.8445-0.2931.29810.67841.47-0.0828-0.0280.1634-0.1985-0.17840.2804-0.3009-0.0558-0.00130.23580.02150.02090.22830.04560.2165-41.883619.3447-6.166
101.3622-0.25660.28841.64610.48220.94850.05160.03560.09950.02960.1321-0.0883-0.3830.61090.00070.2716-0.09760.03180.4206-0.02890.30175.809326.114727.231
111.3298-0.49240.1632.25430.38261.28330.09640.1378-0.3189-0.06570.00770.0720.18350.1113-00.18330.0017-0.0290.2265-0.00330.3857-7.05475.047515.5533
120.98380.24650.70981.56390.79611.18740.03970.1515-0.25840.04870.1513-0.22970.07430.42040.01070.20780.02910.01460.3617-0.01280.3175-1.535514.996222.303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1530 - 1645
2X-RAY DIFFRACTION2A1646 - 1803
3X-RAY DIFFRACTION3A1804 - 1862
4X-RAY DIFFRACTION4B1530 - 1630
5X-RAY DIFFRACTION5B1631 - 1803
6X-RAY DIFFRACTION6B1804 - 1860
7X-RAY DIFFRACTION7C1530 - 1627
8X-RAY DIFFRACTION8C1628 - 1801
9X-RAY DIFFRACTION9C1802 - 1861
10X-RAY DIFFRACTION10D1530 - 1627
11X-RAY DIFFRACTION11D1628 - 1771
12X-RAY DIFFRACTION12D1780 - 1861

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