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- PDB-5tz5: Crystal Structure of CurK Dehydratase H996F Inactive Mutant -

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Basic information

Entry
Database: PDB / ID: 5tz5
TitleCrystal Structure of CurK Dehydratase H996F Inactive Mutant
ComponentsCurK
KeywordsLYASE / dehydratase / curacin / polyketide synthase
Function / homology
Function and homology information


organic substance biosynthetic process / acyltransferase activity / phosphopantetheine binding / oxidoreductase activity
Similarity search - Function
: / Beta-ketoacyl synthase-like, N-terminal / Polyketide synthase dehydratase / Zinc-binding dehydrogenase / : / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH ...: / Beta-ketoacyl synthase-like, N-terminal / Polyketide synthase dehydratase / Zinc-binding dehydrogenase / : / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Thiol Ester Dehydrase; Chain A / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / 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 / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesMoorea producens 3L (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.428 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 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CurK
B: CurK


Theoretical massNumber of molelcules
Total (without water)65,4482
Polymers65,4482
Non-polymers00
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-1 kcal/mol
Surface area25660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.113, 94.567, 152.003
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CurK / Polyketide synthase module


Mass: 32723.859 Da / Num. of mol.: 2 / Mutation: H996F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorea producens 3L (bacteria) / Gene: LYNGBM3L_74450 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pRARE AI / References: UniProt: F4Y425
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.3 M Tri-Sodium Citrate, 30mm D(+) sucrose, 100mm tris ph 8.5

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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: 1.428→40.15 Å / Num. obs: 100090 / % possible obs: 97 % / Redundancy: 13 % / CC1/2: 1 / Net I/σ(I): 28.15
Reflection shellResolution: 1.428→1.479 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 2.74 / CC1/2: 0.832 / % possible all: 87

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 3kg9

3kg9


Resolution: 1.428→40.148 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 4989 4.98 %
Rwork0.1872 95099 -
obs0.1884 100088 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.84 Å2 / Biso mean: 28.3549 Å2 / Biso min: 11.45 Å2
Refinement stepCycle: final / Resolution: 1.428→40.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4383 0 0 168 4551
Biso mean---27.87 -
Num. residues----560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134525
X-RAY DIFFRACTIONf_angle_d1.2716152
X-RAY DIFFRACTIONf_chiral_restr0.109720
X-RAY DIFFRACTIONf_plane_restr0.008794
X-RAY DIFFRACTIONf_dihedral_angle_d21.6011660
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 (%)
1.4284-1.44460.28361410.25342477261878
1.4446-1.46160.23311440.24042888303288
1.4616-1.47950.2871720.22553021319395
1.4795-1.49820.22921730.21343074324796
1.4982-1.51790.23811900.21243074326496
1.5179-1.53870.24451500.20053154330498
1.5387-1.56070.23231590.19163101326097
1.5607-1.5840.22861600.1893136329696
1.584-1.60870.24341710.18563149332099
1.6087-1.63510.22661600.18853169332997
1.6351-1.66330.22221620.1793145330796
1.6633-1.69360.19841750.185731703345100
1.6936-1.72610.23681560.18043157331396
1.7261-1.76140.20911780.183145332399
1.7614-1.79970.19951520.17593178333098
1.7997-1.84150.21761700.18773170334098
1.8415-1.88760.20721640.19493248341299
1.8876-1.93860.22241650.19213151331698
1.9386-1.99570.21681760.1913215339198
1.9957-2.06010.21311440.18673230337499
2.0601-2.13370.20691980.19243189338798
2.1337-2.21910.20161560.182232653421100
2.2191-2.32010.20271580.19193233339199
2.3201-2.44240.24821840.19613226341099
2.4424-2.59540.23931570.20093283344099
2.5954-2.79580.21341790.204932833462100
2.7958-3.0770.23651550.206133143469100
3.077-3.5220.18451640.191733553519100
3.522-4.43650.19151820.160333533535100
4.4365-40.16370.19931940.173835463740100
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)
11.3039-0.4025-0.09711.7323-0.90172.2745-0.0361-0.0838-0.0820.0496-0.04690.03410.1992-0.0123-0.03570.1481-0.0050.02430.11980.00510.160513.279819.5181-22.617
22.11790.97860.56472.32710.21541.79570.0117-0.095-0.05490.0149-0.06710.1760.138-0.08750.02740.117-0.00230.01410.1720.00050.169918.833122.2556-26.5279
32.37631.08680.12312.62490.45881.3658-0.0466-0.0312-0.30150.11610.0842-0.25120.18890.13460.06390.16640.0259-0.00420.14020.00770.172922.335216.8225-23.0298
40.0717-0.38320.06711.6264-0.30981.04810.0985-0.08130.3177-0.1401-0.044-0.2839-0.53440.20230.24970.2532-0.143-0.02120.31660.09740.32818.445746.0197-39.2617
51.08390.12030.07021.342-0.19821.6849-0.00510.16880.0783-0.17450.05830.1307-0.0078-0.1337-0.04860.1359-0.012-0.02470.16770.02520.17886.337932.9263-37.7453
61.5116-0.27380.13342.0848-0.30372.0960.02490.3040.0336-0.2909-0.0621-0.03890.0860.05690.05810.1578-0.01010.00280.21680.02020.169117.378732.8747-38.6791
70.81620.2779-0.09091.0677-1.4033.39090.11040.24430.06-0.6093-0.3443-0.20030.1590.18190.00470.35380.10560.0850.19730.06870.116518.46363.1855-9.5916
81.4876-0.4991-0.31261.7563-0.22342.09010.04270.05580.0315-0.1757-0.0798-0.06680.0539-0.06310.04660.15540.00030.04020.12710.03240.1420.7855-1.75224.7403
91.6738-0.0203-0.72942.87530.65643.7152-0.00050.267-0.1166-0.7106-0.286-0.34110.20990.1409-0.42840.36110.07180.15690.18550.06660.184626.309-0.0293-7.5924
100.7911-0.10350.05841.8604-0.78121.65260.0173-0.0081-0.1142-0.1302-0.1278-0.15480.20830.14940.08520.1810.01190.04590.20390.02760.198725.1642-12.179712.7255
111.1372-0.2338-0.32572.1425-0.37352.1108-0.017-0.1515-0.01180.04430.005-0.11760.07060.07950.04860.1784-0.02550.02990.17540.00620.188522.0209-12.183416.266
121.0094-0.6381-0.282.1477-0.38352.6150.0346-0.02920.0045-0.1497-0.1084-0.28480.16140.20550.08080.18830.00110.03830.1750.03460.17327.1181-15.65319.002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 962 through 1019 )A962 - 1019
2X-RAY DIFFRACTION2chain 'A' and (resid 1020 through 1044 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1045 through 1089 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1090 through 1112 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1113 through 1179 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1180 through 1247 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 962 through 985 )B962 - 985
8X-RAY DIFFRACTION8chain 'B' and (resid 986 through 1045 )B986 - 1045
9X-RAY DIFFRACTION9chain 'B' and (resid 1046 through 1067 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1068 through 1123 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 1124 through 1194 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 1195 through 1250 )B0

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