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- PDB-5tz6: Crystal Structure of CurJ Dehydratase H978F Inactive Mutant In Co... -

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Basic information

Entry
Database: PDB / ID: 5tz6
TitleCrystal Structure of CurJ Dehydratase H978F Inactive Mutant In Complex with Compound 21
ComponentsCurJ
Keywordslyase/lyase inhibitor / dehydratase / curacin / polyketide synthase / lyase-lyase inhibitor complex
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Thiol Ester Dehydrase; Chain A - #120 / Methyltransferase, Helix-turn-helix domain / : / Beta-ketoacyl synthase-like, N-terminal / CurL-like, PKS C-terminal / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain ...Thiol Ester Dehydrase; Chain A - #120 / Methyltransferase, Helix-turn-helix domain / : / Beta-ketoacyl synthase-like, N-terminal / CurL-like, PKS C-terminal / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / PKS_PP_betabranch / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / 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 / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
(2E,5R)-5-hydroxy-2-methylhept-2-enoic acid / CurJ
Similarity search - Component
Biological speciesMoorea producens 3L (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDodge, G.J. / Smith, J.L.
CitationJournal: J. Am. Chem. Soc. / Year: 2016
Title: Vinylogous Dehydration by a Polyketide Dehydratase Domain in Curacin Biosynthesis.
Authors: Fiers, W.D. / Dodge, G.J. / Sherman, D.H. / Smith, J.L. / Aldrich, C.C.
History
DepositionNov 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: CurJ
B: CurJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3263
Polymers69,1682
Non-polymers1581
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-12 kcal/mol
Surface area26040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.550, 70.584, 176.018
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 (resseq 943:1051 or resseq 1066:1082 or resseq...
21(chain B and (resseq 943:1051 or resseq 1066:1082 or resseq...

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
11THRTHRLEULEU(chain A and (resseq 943:1051 or resseq 1066:1082 or resseq...AA943 - 10516 - 114
12SERSERGLUGLU(chain A and (resseq 943:1051 or resseq 1066:1082 or resseq...AA1066 - 1082129 - 145
13PROPROASPASP(chain A and (resseq 943:1051 or resseq 1066:1082 or resseq...AA1087 - 1168150 - 231
14ASNASNPROPRO(chain A and (resseq 943:1051 or resseq 1066:1082 or resseq...AA1172 - 1179235 - 242
15PHEPHEPHEPHE(chain A and (resseq 943:1051 or resseq 1066:1082 or resseq...AA1180243
16THRTHRMETMET(chain A and (resseq 943:1051 or resseq 1066:1082 or resseq...AA943 - 12446 - 307
17THRTHRMETMET(chain A and (resseq 943:1051 or resseq 1066:1082 or resseq...AA943 - 12446 - 307
18THRTHRMETMET(chain A and (resseq 943:1051 or resseq 1066:1082 or resseq...AA943 - 12446 - 307
19THRTHRMETMET(chain A and (resseq 943:1051 or resseq 1066:1082 or resseq...AA943 - 12446 - 307
110THRTHRMETMET(chain A and (resseq 943:1051 or resseq 1066:1082 or resseq...AA943 - 12446 - 307
111THRTHRMETMET(chain A and (resseq 943:1051 or resseq 1066:1082 or resseq...AA943 - 12446 - 307
112THRTHRMETMET(chain A and (resseq 943:1051 or resseq 1066:1082 or resseq...AA943 - 12446 - 307
113THRTHRMETMET(chain A and (resseq 943:1051 or resseq 1066:1082 or resseq...AA943 - 12446 - 307
21THRTHRLEULEU(chain B and (resseq 943:1051 or resseq 1066:1082 or resseq...BB943 - 10516 - 114
22SERSERGLUGLU(chain B and (resseq 943:1051 or resseq 1066:1082 or resseq...BB1066 - 1082129 - 145
23PROPROASPASP(chain B and (resseq 943:1051 or resseq 1066:1082 or resseq...BB1087 - 1168150 - 231
24ASNASNPROPRO(chain B and (resseq 943:1051 or resseq 1066:1082 or resseq...BB1172 - 1179235 - 242
25PHEPHEPHEPHE(chain B and (resseq 943:1051 or resseq 1066:1082 or resseq...BB1180243
26THRTHRMETMET(chain B and (resseq 943:1051 or resseq 1066:1082 or resseq...BB943 - 12446 - 307
27THRTHRMETMET(chain B and (resseq 943:1051 or resseq 1066:1082 or resseq...BB943 - 12446 - 307
28THRTHRMETMET(chain B and (resseq 943:1051 or resseq 1066:1082 or resseq...BB943 - 12446 - 307
29THRTHRMETMET(chain B and (resseq 943:1051 or resseq 1066:1082 or resseq...BB943 - 12446 - 307
210THRTHRMETMET(chain B and (resseq 943:1051 or resseq 1066:1082 or resseq...BB943 - 12446 - 307
211THRTHRMETMET(chain B and (resseq 943:1051 or resseq 1066:1082 or resseq...BB943 - 12446 - 307
212THRTHRMETMET(chain B and (resseq 943:1051 or resseq 1066:1082 or resseq...BB943 - 12446 - 307
213THRTHRMETMET(chain B and (resseq 943:1051 or resseq 1066:1082 or resseq...BB943 - 12446 - 307

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Components

#1: Protein CurJ / Polyketide synthase module


Mass: 34583.988 Da / Num. of mol.: 2 / Mutation: H978F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorea producens 3L (bacteria) / Gene: LYNGBM3L_74460 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pRARE AI / References: UniProt: F4Y426
#2: Chemical ChemComp-7OD / (2E,5R)-5-hydroxy-2-methylhept-2-enoic acid


Mass: 158.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% peg 3350, 5% 1,4 butanediol, 250mm nacl, 100mm bis-tris propane ph 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2015
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.4→45.905 Å / Num. obs: 23985 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.999 / Net I/σ(I): 18.08
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 2.07 / CC1/2: 0.774 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kg8

3kg8


Resolution: 2.4→45.905 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.86
RfactorNum. reflection% reflection
Rfree0.2422 1989 8.31 %
Rwork0.1985 --
obs0.2021 23944 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 287.31 Å2 / Biso mean: 114.9129 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.4→45.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4554 0 24 33 4611
Biso mean--112.14 88.42 -
Num. residues----571
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2724X-RAY DIFFRACTION6.176TORSIONAL
12B2724X-RAY DIFFRACTION6.176TORSIONAL
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)
17.3086-1.71134.15854.1031-4.34276.0787-0.0699-0.36331.0940.902-0.0866-0.3771-0.28080.51810.16420.5333-0.0635-0.12690.6674-0.27690.7446-2.35920.017918.581
25.0748-0.43610.29544.28020.40212.9369-0.1294-0.21650.39160.28230.1-0.1282-0.1408-0.0382-0.00690.25890.027-0.0460.4664-0.07070.5649-10.3253-3.70299.825
37.08653.08981.65787.2049-1.64937.13610.6571-0.7354-0.06461.33-0.17770.64070.1852-0.5763-0.54680.5830.00930.06350.5357-0.07630.7893-5.7535-10.910514.3964
47.6112-4.77836.16995.0933-3.8195.297-0.64611.24913.4899-0.8225-0.4058-0.2303-0.8441.01811.04450.9860.03690.03991.0370.25881.1644-16.911111.0579-13.7248
56.48840.9951-0.0463.7298-0.94854.3395-0.0250.0770.5708-0.2227-0.03510.9478-0.1846-0.49620.180.36310.0767-0.10450.4838-0.04430.7703-27.58361.436-3.8601
66.55410.34721.12562.8716-0.1823.415-0.0307-0.09510.3019-0.1685-0.18070.3617-0.2916-0.46280.19190.28420.04360.05160.38860.02180.6395-20.6657-0.8609-0.56
78.60621.73551.14528.406-0.90846.3260.13110.05271.41620.1761-0.34620.2159-0.37630.02140.23350.3495-0.06530.01490.44170.10180.7515-13.64647.3754-5.1225
89.3891.53180.66478.6652-0.55187.5821-0.35281.1764-0.4247-1.0790.2512-1.07680.59690.3880.12250.370.03980.07750.5624-0.00960.5363-14.5767-5.8283-12.3122
98.62721.80690.10082.75870.00664.67640.05640.03070.5028-0.3578-0.04880.4353-0.030.06370.22290.21090.0403-0.04850.4639-0.03540.4426-15.7381-2.7321-3.1732
107.14272.13623.69985.68362.12258.6386-0.1459-0.45120.60681.7841-0.2694-0.74850.02180.08380.22890.94220.0377-0.43080.7474-0.11930.88028.5666-1.645334.5409
113.145-1.73821.7262.0347-3.34494.7215-0.3906-0.67070.5511.57190.2927-0.2886-1.70220.56420.081.9115-0.1891-0.47781.2306-0.15841.296715.6381-0.42353.6309
121.3768-2.4362-0.06664.01480.48993.2238-0.033-1.61540.37222.59010.163-1.49050.43230.4388-0.01182.39240.0253-0.78181.5571-0.08261.186416.1703-3.801150.9263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 943 through 967 )A943 - 967
2X-RAY DIFFRACTION2chain 'A' and (resid 968 through 1047 )A968 - 1047
3X-RAY DIFFRACTION3chain 'A' and (resid 1048 through 1078 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1079 through 1100 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1101 through 1137 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1138 through 1182 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1183 through 1204 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 1205 through 1219 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 1220 through 1244 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 943 through 1048 )B943 - 1048
11X-RAY DIFFRACTION11chain 'B' and (resid 1049 through 1137 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 1138 through 1244 )B0

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