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- PDB-7l4l: Crosslinked Crystal Structure of Type II Fatty Acid Synthase Keto... -

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Basic information

Entry
Database: PDB / ID: 7l4l
TitleCrosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabF, and C8-crypto Acyl Carrier Protein, AcpP
Components
  • 3-oxoacyl-[acyl-carrier-protein] synthase 2
  • Acyl carrier protein
KeywordsTRANSFERASE / Thiolase / ketosynthase / KS / AcpP / ACP
Function / homology
Function and homology information


fatty acid elongation, saturated fatty acid / monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase II / lipid A biosynthetic process / lipid biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / response to cold ...fatty acid elongation, saturated fatty acid / monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase II / lipid A biosynthetic process / lipid biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / response to cold / fatty acid biosynthetic process / response to xenobiotic stimulus / lipid binding / protein homodimerization activity / membrane / cytoplasm / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Acyl carrier protein (ACP) / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-DYF / Acyl carrier protein / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsMindrebo, J.T. / Chen, A. / Kim, W.E. / Burkart, M.D. / Noel, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)095970-09 United States
CitationJournal: Acs Catalysis / Year: 2021
Title: Structure and Mechanistic Analyses of the Gating Mechanism of Elongating Ketosynthases
Authors: Mindrebo, J.T. / Chen, A. / Kim, W.E. / Re, R.N. / Davis, T.D. / Noel, J.P. / Burkart, M.D.
History
DepositionDec 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
C: Acyl carrier protein
D: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4478
Polymers103,4704
Non-polymers9774
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10420 Å2
ΔGint-63 kcal/mol
Surface area31810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.782, 92.136, 113.746
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 126 or resid 128...
21(chain B and (resid 2 through 63 or (resid 64...

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
11LYSLYSPROPRO(chain A and (resid 2 through 126 or resid 128...AA2 - 1263 - 127
12LYSLYSASPASP(chain A and (resid 2 through 126 or resid 128...AA128 - 223129 - 224
13LYSLYSLYSLYS(chain A and (resid 2 through 126 or resid 128...AA224225
14SERSERILEILE(chain A and (resid 2 through 126 or resid 128...AA1 - 4122 - 413
15SERSERILEILE(chain A and (resid 2 through 126 or resid 128...AA1 - 4122 - 413
16SERSERILEILE(chain A and (resid 2 through 126 or resid 128...AA1 - 4122 - 413
21LYSLYSSERSER(chain B and (resid 2 through 63 or (resid 64...BB2 - 633 - 64
22ARGARGARGARG(chain B and (resid 2 through 63 or (resid 64...BB6465
23LYSLYSILEILE(chain B and (resid 2 through 63 or (resid 64...BB2 - 4123 - 413

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 2 / 3-oxoacyl-[acyl-carrier-protein] synthase II / Beta-ketoacyl-ACP synthase II / KAS II


Mass: 43089.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fabF, fabJ, b1095, JW1081 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AAI5, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Protein Acyl carrier protein / ACP / Cytosolic-activating factor / CAF / Fatty acid synthase acyl carrier protein


Mass: 8645.460 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: acpP, b1094, JW1080 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A6A8
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-DYF / [(3~{R})-2,2-dimethyl-4-[[3-[2-[[(~{E})-oct-2-enoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate


Mass: 465.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H36N3O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 42.02 % / Mosaicity: 0.13 °
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30 % PEG 8K, 0.1 M sodium cacodylate pH 6.5, and 0.3 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→48.4 Å / Num. obs: 26271 / % possible obs: 100 % / Redundancy: 13.9 % / Biso Wilson estimate: 36.83 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.404 / Rpim(I) all: 0.112 / Rrim(I) all: 0.42 / Net I/σ(I): 7.5 / Num. measured all: 364390 / Scaling rejects: 78
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.65-2.7814.81.8995089934280.7280.5081.9661.8100
8.79-48.411.60.08494498160.9980.0250.08820.899.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OKG

6okg


Resolution: 2.65→48.396 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2665 1299 4.96 %
Rwork0.2221 24904 -
obs0.2243 26203 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.95 Å2 / Biso mean: 47.1609 Å2 / Biso min: 13.64 Å2
Refinement stepCycle: final / Resolution: 2.65→48.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7070 0 62 133 7265
Biso mean--44.53 34.85 -
Num. residues----973
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3583X-RAY DIFFRACTION7.353TORSIONAL
12B3583X-RAY DIFFRACTION7.353TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.65-2.75610.36961470.30222702
2.7561-2.88150.29411270.2882761
2.8815-3.03340.27491330.26932710
3.0334-3.22350.32831390.26222748
3.2235-3.47230.31281420.24462741
3.4723-3.82160.27981650.22422739
3.8216-4.37430.23181340.20272777
4.3743-5.50990.24381660.18762776
5.5099-48.3960.20491460.17372950
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)
10.6526-0.1345-0.10822.9922-1.02772.33070.08610.28810.1323-0.171-0.1713-0.04710.34460.33690.00840.2430.0819-0.01270.42990.02380.218225.3677.7715-3.2048
22.1178-0.61660.4432.7897-0.17552.43860.03330.0821-0.1005-0.34460.15930.29890.6886-0.3147-0.07070.415-0.0319-0.10140.24870.03520.253916.4377-1.94983.4839
30.9097-0.33640.40550.9778-0.03311.84890.02310.1625-0.0344-0.30940.04170.04710.40380.5771-0.03010.36660.14910.01960.4025-0.04330.226431.1680.73475.2852
41.1461-1.018-0.67980.90510.61921.05030.1210.15180.0732-0.06390.026-0.19170.25920.7227-0.13790.25420.22050.04320.6367-0.11930.343142.13924.960719.902
50.6434-0.26180.23790.2447-0.32280.47040.02890.09970.06780.0151-0.0497-0.29630.20480.80390.04430.20940.08430.00230.86980.04170.370246.96328.710211.2399
61.1338-0.1580.11620.8909-0.56110.82770.05480.1590.1514-0.1809-0.3-0.48130.15441.155-0.0540.24470.08030.08110.96810.07260.370345.198310.88631.6122
70.67680.0925-0.15270.748-0.18680.07150.18780.19850.1491-0.2387-0.2288-0.01270.42020.82120.00540.36090.22710.01270.76480.00340.301241.52910.96969.0883
81.8909-0.55640.81732.0454-1.0421.7710.144-0.49890.0560.32620.18170.20370.4751-0.4677-0.26480.4298-0.11770.00620.41510.03340.220713.6412-3.977432.1476
92.2635-2.06120.98864.2885-1.574.62330.087-0.2240.16270.09780.043-0.0069-0.04040.0174-0.08380.1268-0.05380.0280.2161-0.04590.205823.22695.065925.4074
100.4709-0.14110.09210.6811-0.16442.45710.3440.0059-0.0606-0.10610.08230.22681.0735-0.3393-0.160.451-0.0665-0.0830.2950.07680.313917.0346-7.242621.8386
110.08580.00430.08860.7086-0.47851.35920.15970.0284-0.1764-0.1271-0.0224-0.251.18730.4722-0.33050.77980.1705-0.15310.37-0.01380.405632.0785-16.803328.7758
120.4256-0.21920.76350.4798-0.31291.41150.254-0.0569-0.2429-0.08430.08440.08011.0216-0.084-0.10291.291-0.1382-0.30570.404-0.03020.339417.1266-20.9839.0875
130.6880.1020.10790.24120.070.62840.35240.0964-0.3858-0.16930.07160.09781.0978-0.2420.17081.4017-0.3704-0.33170.30510.12620.519713.3685-26.647217.7797
141.07780.3089-0.19571.0754-0.55741.07210.1585-0.0193-0.3849-0.09770.03390.20051.4575-0.6545-0.30861.2749-0.413-0.24440.42540.12560.504111.0599-23.316527.8369
150.03560.10510.07590.9711-0.57411.16050.2-0.1768-0.12720.09630.0330.01791.151-0.0366-0.34151.0926-0.0559-0.18370.22850.03390.406521.4049-20.4520.4575
160.41-0.2140.52811.5348-0.52730.7225-0.1828-0.10230.0474-0.26210.41340.6002-0.4741-1.0779-0.20270.8221-0.0837-0.22011.41580.33840.5599-7.20152.1022-8.7455
170.45150.54880.27440.66220.33230.16680.2228-0.1309-0.56950.3318-0.0296-0.22230.4936-0.53-0.12360.9936-0.6804-0.35621.45640.2710.8794-5.612-8.3106-10.6182
187.2172.4648-0.32454.51884.575.9740.30190.3206-0.0947-0.42940.15890.51370.8323-1.292-0.49740.7644-0.3923-0.27910.99130.32870.5116-3.0463-2.3120.0659
192.22410.9919-0.37671.82290.53570.42260.05220.32680.33980.08370.05780.68440.3907-1.097-0.13690.75-0.4969-0.03521.7390.54151.0258-13.5588-1.46611.688
206.7307-3.2674-0.58398.76911.42164.45870.0265-0.69730.51911.06160.15590.3859-1.6649-0.5846-0.23130.87540.04760.09320.4728-0.1440.491320.806328.50739.4363
219.06542.18973.1572.892-0.38721.6597-0.3314-0.1460.6340.63480.2838-0.3415-1.15070.91940.10610.5302-0.1611-0.03060.3565-0.03760.442331.845925.553434.6902
226.6633-4.16624.50136.0394-2.10033.2937-0.0824-0.1555-0.39090.22630.49421.0292-1.1025-0.302-0.06690.43320.00920.16450.3168-0.0540.501120.484125.41426.9212
235.56411.7116-4.67211.772-0.84064.20870.02880.76620.4622-0.19780.26881.0952-1.325-1.4131-0.30691.07560.3914-0.0820.63850.03320.549516.329934.076223.7697
240.5756-0.6306-0.01571.4654-0.7291.22240.24440.26930.3332-1.3265-0.23850.1202-0.9753-0.2087-0.09821.70160.0087-0.07720.3282-0.0750.664625.187935.792527.8842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 71 )A2 - 71
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 138 )A72 - 138
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 264 )A139 - 264
4X-RAY DIFFRACTION4chain 'A' and (resid 265 through 290 )A265 - 290
5X-RAY DIFFRACTION5chain 'A' and (resid 291 through 322 )A291 - 322
6X-RAY DIFFRACTION6chain 'A' and (resid 323 through 391 )A323 - 391
7X-RAY DIFFRACTION7chain 'A' and (resid 392 through 412 )A392 - 412
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 71 )B2 - 71
9X-RAY DIFFRACTION9chain 'B' and (resid 72 through 138 )B72 - 138
10X-RAY DIFFRACTION10chain 'B' and (resid 139 through 233 )B139 - 233
11X-RAY DIFFRACTION11chain 'B' and (resid 234 through 264 )B234 - 264
12X-RAY DIFFRACTION12chain 'B' and (resid 265 through 290 )B265 - 290
13X-RAY DIFFRACTION13chain 'B' and (resid 291 through 326 )B291 - 326
14X-RAY DIFFRACTION14chain 'B' and (resid 327 through 391 )B327 - 391
15X-RAY DIFFRACTION15chain 'B' and (resid 392 through 412 )B392 - 412
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 15 )C1 - 15
17X-RAY DIFFRACTION17chain 'C' and (resid 16 through 30 )C16 - 30
18X-RAY DIFFRACTION18chain 'C' and (resid 31 through 49 )C31 - 49
19X-RAY DIFFRACTION19chain 'C' and (resid 50 through 75 )C50 - 75
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 24 )D1 - 24
21X-RAY DIFFRACTION21chain 'D' and (resid 25 through 35 )D25 - 35
22X-RAY DIFFRACTION22chain 'D' and (resid 36 through 49 )D36 - 49
23X-RAY DIFFRACTION23chain 'D' and (resid 50 through 55 )D50 - 55
24X-RAY DIFFRACTION24chain 'D' and (resid 56 through 75 )D56 - 75

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